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Plachetzki DC, Pankey MS, MacManes MD, Lesser MP, Walker CW. The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis. Genome Biol Evol 2020; 12:1681-1693. [PMID: 32653903 PMCID: PMC7531772 DOI: 10.1093/gbe/evaa143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Apoptosis is a fundamental feature of multicellular animals and is best understood in mammals, flies, and nematodes, with the invertebrate models being thought to represent a condition of ancestral simplicity. However, the existence of a leukemia-like cancer in the softshell clam Mya arenaria provides an opportunity to re-evaluate the evolution of the genetic machinery of apoptosis. Here, we report the whole-genome sequence for M. arenaria which we leverage with existing data to test evolutionary hypotheses on the origins of apoptosis in animals. We show that the ancestral bilaterian p53 locus, a master regulator of apoptosis, possessed a complex domain structure, in contrast to that of extant ecdysozoan p53s. Further, ecdysozoan taxa, but not chordates or lophotrochozoans like M. arenaria, show a widespread reduction in apoptosis gene copy number. Finally, phylogenetic exploration of apoptosis gene copy number reveals a striking linkage with p53 domain complexity across species. Our results challenge the current understanding of the evolution of apoptosis and highlight the ancestral complexity of the bilaterian apoptotic tool kit and its subsequent dismantlement during the ecdysozoan radiation.
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Affiliation(s)
- David C Plachetzki
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire
| | - M Sabrina Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire
| | - Matthew D MacManes
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire
| | - Michael P Lesser
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire
- School of Marine Science and Ocean Engineering, University of New Hampshire
| | - Charles W Walker
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire
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Budd GE, Jensen S. The origin of the animals and a 'Savannah' hypothesis for early bilaterian evolution. Biol Rev Camb Philos Soc 2015; 92:446-473. [PMID: 26588818 DOI: 10.1111/brv.12239] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 12/14/2022]
Abstract
The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the 'Cambrian explosion', is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so-called 'Ediacaran' taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total-group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran-Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat-dominated substrates that the enigmatic Ediacaran taxa were associated with, the so-called 'Cambrian substrate revolution', leading to the loss of almost all Ediacara-aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late-Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara-style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.
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Affiliation(s)
- Graham E Budd
- Palaeobiology Programme, Department of Earth Sciences, Uppsala University, Villavägen 16, SE 752 40, Uppsala, Sweden
| | - Sören Jensen
- Área de Paleontología, Facultad de Ciencias, Universidad de Extremadura, 06006, Badajoz, Spain
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Borner J, Rehm P, Schill RO, Ebersberger I, Burmester T. A transcriptome approach to ecdysozoan phylogeny. Mol Phylogenet Evol 2014; 80:79-87. [PMID: 25124096 DOI: 10.1016/j.ympev.2014.08.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/15/2014] [Accepted: 08/01/2014] [Indexed: 11/20/2022]
Abstract
The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns.
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Affiliation(s)
- Janus Borner
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
| | - Peter Rehm
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
| | - Ralph O Schill
- Zoology, Biological Institute, University of Stuttgart, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, University of Frankfurt, Institute for Cell Biology and Neuroscience, Germany
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.
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Gallegos ME, Balakrishnan S, Chandramouli P, Arora S, Azameera A, Babushekar A, Bargoma E, Bokhari A, Chava SK, Das P, Desai M, Decena D, Saramma SDD, Dey B, Doss AL, Gor N, Gudiputi L, Guo C, Hande S, Jensen M, Jones S, Jones N, Jorgens D, Karamchedu P, Kamrani K, Kolora LD, Kristensen L, Kwan K, Lau H, Maharaj P, Mander N, Mangipudi K, Menakuru H, Mody V, Mohanty S, Mukkamala S, Mundra SA, Nagaraju S, Narayanaswamy R, Ndungu-Case C, Noorbakhsh M, Patel J, Patel P, Pendem SV, Ponakala A, Rath M, Robles MC, Rokkam D, Roth C, Sasidharan P, Shah S, Tandon S, Suprai J, Truong TQN, Uthayaruban R, Varma A, Ved U, Wang Z, Yu Z. The C. elegans rab family: identification, classification and toolkit construction. PLoS One 2012; 7:e49387. [PMID: 23185324 PMCID: PMC3504004 DOI: 10.1371/journal.pone.0049387] [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: 01/24/2012] [Accepted: 10/09/2012] [Indexed: 11/29/2022] Open
Abstract
Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB).
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Affiliation(s)
- Maria E Gallegos
- Department of Biological Sciences, California State University East Bay, Hayward, CA, USA.
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Telford MJ, Copley RR. Improving animal phylogenies with genomic data. Trends Genet 2011; 27:186-95. [DOI: 10.1016/j.tig.2011.02.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 02/04/2023]
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Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: recent progress and remaining questions. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0044-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Holton TA, Pisani D. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2010; 2:310-24. [PMID: 20624736 PMCID: PMC2997542 DOI: 10.1093/gbe/evq016] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman’s Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, supporting instead the rearrangement of the protostomes into two new clades: the Lophotrochozoa (including, e.g., the molluscs and the annelids) and the Ecdysozoa (including the Panarthropoda and most pseudocoelomates, such as the nematodes and priapulids). Support for this new animal phylogeny has been attained from expressed sequence tag studies, although these generally have a limited gene sampling. In contrast, deep genomic-scale analyses have often supported Coelomata. However, these studies are problematic due to their limited taxonomic sampling, which could exacerbate tree reconstruction artifacts. Here, we address both of these sampling limitations; we study the effect of long-branch attraction (LBA) in deep genomic-scale analyses and provide convincing evidence, using both single- and multigene families, that Coelomata is an artifact. We show that optimal outgroup selection is key in avoiding LBA and identify the use of inadequate outgroups as the reason previous deep genomic-scale analyses found strong support for Coelomata.
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Affiliation(s)
- Thérèse A Holton
- Department of Biology, National University of Ireland, Maynooth, Maynooth Co. Kildare, Ireland
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Zarlenga DS, Gasbarre LC. From parasite genomes to one healthy world: Are we having fun yet? Vet Parasitol 2009; 163:235-49. [PMID: 19560277 DOI: 10.1016/j.vetpar.2009.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In 1990, the Human Genome Sequencing Project was established. This laid the ground work for an explosion of sequence data that has since followed. As a result of this effort, the first complete genome of an animal, Caenorhabditis elegans was published in 1998. The sequence of Drosophila melanogaster was made available in March, 2000 and in the following year, working drafts of the human genome were generated with the completed sequence (92%) being released in 2003. Recent advancements and next-generation technologies have made sequencing common place and have infiltrated every aspect of biological research, including parasitology. To date, sequencing of 32 apicomplexa and 24 nematode genomes are either in progress or near completion, and over 600k nematode EST and 200k apicomplexa EST submissions fill the databases. However, the winds have shifted and efforts are now refocusing on how best to store, mine and apply these data to problem solving. Herein we tend not to summarize existing X-omics datasets or present new technological advances that promise future benefits. Rather, the information to follow condenses up-to-date-applications of existing technologies to problem solving as it relates to parasite research. Advancements in non-parasite systems are also presented with the proviso that applications to parasite research are in the making.
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Affiliation(s)
- Dante S Zarlenga
- USDA, ARS, ANRI Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA.
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9
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Abstract
The past two decades have witnessed profound changes in our understanding of the evolution of arthropods. Many of these insights derive from the adoption of molecular methods by systematists and developmental biologists, prompting a radical reordering of the relationships among extant arthropod classes and their closest non-arthropod relatives, and shedding light on the developmental basis for the origins of key characteristics. A complementary source of data is the discovery of fossils from several spectacular Cambrian faunas. These fossils form well-characterized groupings, making the broad pattern of Cambrian arthropod systematics increasingly consensual.
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Telford MJ, Bourlat SJ, Economou A, Papillon D, Rota-Stabelli O. The evolution of the Ecdysozoa. Philos Trans R Soc Lond B Biol Sci 2008; 363:1529-37. [PMID: 18192181 DOI: 10.1098/rstb.2007.2243] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.
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Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol Direct 2008; 3:7. [PMID: 18346278 PMCID: PMC2292158 DOI: 10.1186/1745-6150-3-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 03/17/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rare genomic changes (RGCs) that are thought to comprise derived shared characters of individual clades are becoming an increasingly important class of markers in genome-wide phylogenetic studies. Recently, we proposed a new type of RGCs designated RGC_CAMs (after Conserved Amino acids-Multiple substitutions) that were inferred using genome-wide identification of amino acid replacements that were: i) located in unambiguously aligned regions of orthologous genes, ii) shared by two or more taxa in positions that contain a different, conserved amino acid in a much broader range of taxa, and iii) require two or three nucleotide substitutions. When applied to animal phylogeny, the RGC_CAM approach supported the coelomate clade that unites deuterostomes with arthropods as opposed to the ecdysozoan (molting animals) clade. However, a non-negligible level of homoplasy was detected. RESULTS We provide a direct estimate of the level of homoplasy caused by parallel changes and reversals among the RGC_CAMs using 462 alignments of orthologous genes from 19 eukaryotic species. It is shown that the impact of parallel changes and reversals on the results of phylogenetic inference using RGC_CAMs cannot explain the observed support for the Coelomata clade. In contrast, the evidence in support of the Ecdysozoa clade, in large part, can be attributed to parallel changes. It is demonstrated that parallel changes are significantly more common in internal branches of different subtrees that are separated from the respective common ancestor by relatively short times than in terminal branches separated by longer time intervals. A similar but much weaker trend was detected for reversals. The observed evolutionary trend of parallel changes is explained in terms of the covarion model of molecular evolution. As the overlap between the covarion sets in orthologous genes from different lineages decreases with time after divergence, the likelihood of parallel changes decreases as well. CONCLUSION The level of homoplasy observed here appears to be low enough to justify the utility of RGC_CAMs and other types of RGCs for resolution of hard problems in phylogeny. Parallel changes, one of the major classes of events leading to homoplasy, occur much more often in relatively recently diverged lineages than in those separated from their last common ancestor by longer time intervals of time. This pattern seems to provide the molecular-evolutionary underpinning of Vavilov's law of homologous series and is readily interpreted within the framework of the covarion model of molecular evolution.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Karen Thomson
- Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA
| | - Miklós Csürös
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Liran Carmel
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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The tardigrade Hypsibius dujardini, a new model for studying the evolution of development. Dev Biol 2007; 312:545-59. [PMID: 17996863 DOI: 10.1016/j.ydbio.2007.09.055] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 09/12/2007] [Accepted: 09/28/2007] [Indexed: 01/01/2023]
Abstract
Studying development in diverse taxa can address a central issue in evolutionary biology: how morphological diversity arises through the evolution of developmental mechanisms. Two of the best-studied developmental model organisms, the arthropod Drosophila and the nematode Caenorhabditis elegans, have been found to belong to a single protostome superclade, the Ecdysozoa. This finding suggests that a closely related ecdysozoan phylum could serve as a valuable model for studying how developmental mechanisms evolve in ways that can produce diverse body plans. Tardigrades, also called water bears, make up a phylum of microscopic ecdysozoan animals. Tardigrades share many characteristics with C. elegans and Drosophila that could make them useful laboratory models, but long-term culturing of tardigrades historically has been a challenge, and there have been few studies of tardigrade development. Here, we show that the tardigrade Hypsibius dujardini can be cultured continuously for decades and can be cryopreserved. We report that H. dujardini has a compact genome, a little smaller than that of C. elegans or Drosophila, and that sequence evolution has occurred at a typical rate. H. dujardini has a short generation time, 13-14 days at room temperature. We have found that the embryos of H. dujardini have a stereotyped cleavage pattern with asymmetric cell divisions, nuclear migrations, and cell migrations occurring in reproducible patterns. We present a cell lineage of the early embryo and an embryonic staging series. We expect that these data can serve as a platform for using H. dujardini as a model for studying the evolution of developmental mechanisms.
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The Hedgehog gene family of the cnidarian, Nematostella vectensis, and implications for understanding metazoan Hedgehog pathway evolution. Dev Biol 2007; 313:501-18. [PMID: 18068698 DOI: 10.1016/j.ydbio.2007.09.032] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 09/10/2007] [Accepted: 09/10/2007] [Indexed: 11/24/2022]
Abstract
Hedgehog signaling is an important component of cell-cell communication during bilaterian development, and abnormal Hedgehog signaling contributes to disease and birth defects. Hedgehog genes are composed of a ligand ("hedge") domain and an autocatalytic intein ("hog") domain. Hedgehog (hh) ligands bind to a conserved set of receptors and activate downstream signal transduction pathways terminating with Gli/Ci transcription factors. We have identified five intein-containing genes in the anthozoan cnidarian Nematostella vectensis, two of which (NvHh1 and NvHh2) contain definitive hedgehog ligand domains, suggesting that to date, cnidarians are the earliest branching metazoan phylum to possess definitive Hh orthologs. Expression analysis of NvHh1 and NvHh2, the receptor NvPatched, and a downstream transcription factor NvGli (a Gli3/Ci ortholog) indicate that these genes may have conserved roles in planar and trans-epithelial signaling during gut and germline development, while the three remaining intein-containing genes (NvHint1,2,3) are expressed in a cell-type-specific manner in putative neural precursors. Metazoan intein-containing genes that lack a hh ligand domain have previously only been identified within nematodes. However, we have identified intein-containing genes from both Nematostella and in two newly annotated lophotrochozoan genomes. Phylogenetic analyses suggest that while nematode inteins may be derived from an ancestral true hedgehog gene, the newly identified cnidarian and lophotrochozoan inteins may be orthologous, suggesting that both true hedgehog and hint genes may have been present in the cnidarian-bilaterian ancestor. Genomic surveys of N. vectensis suggest that most of the components of both protostome and deuterostome Hh signaling pathways are present in anthozoans and that some appear to have been lost in ecdysozoan lineages. Cnidarians possess many bilaterian cell-cell signaling pathways (Wnt, TGFbeta, FGF, and Hh) that appear to act in concert to pattern tissues along the oral-aboral axis of the polyp. Cnidarians represent a diverse group of animals with a predominantly epithelial body plan, and perhaps selective pressures to pattern epithelia resulted in the ontogeny of the hedgehog pathway in the common ancestor of the Cnidaria and Bilateria.
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Zheng J, Rogozin IB, Koonin EV, Przytycka TM. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 2007; 24:2583-92. [PMID: 17893400 DOI: 10.1093/molbev/msm207] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this method to the analysis of animal phylogeny, obtained support for an Ecdysozoa clade (Roy SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408). The critical assumption in the method was the independence of intron loss in different branches of the phylogenetic tree. Here, this assumption is refuted by showing that the branch-specific intron loss rates are strongly correlated. We show that different tree topologies are obtained, in each case with a significant statistical support, when different subsets of intron positions are analyzed. The analysis of the conserved intron positions supports the Coelomata topology, that is, a clade comprised of arthropods and chordates, whereas the analysis of more variable intron positions favors the Ecdysozoa topology, that is, a clade of arthropods and nematodes. We show, however, that the support for Ecdysozoa is fully explained by parallel loss of introns in nematodes and arthropods, a factor that does not contribute to the analysis of the conserved introns. The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems.
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Affiliation(s)
- Jie Zheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Mukherjee K, Bürglin TR. Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. J Mol Evol 2007; 65:137-53. [PMID: 17665086 DOI: 10.1007/s00239-006-0023-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 11/21/2006] [Indexed: 11/29/2022]
Abstract
TALE homeodomain proteins are an ancient subgroup within the group of homeodomain transcription factors that play important roles in animal, plant, and fungal development. We have extracted the full complement of TALE superclass homeobox genes from the genome projects of seven protostomes, seven deuterostomes, and Nematostella. This was supplemented with TALE homeobox genes from additional species and phylogenetic analyses were carried out with 276 sequences. We found 20 homeobox genes and 4 pseudogenes in humans, 21 genes in mouse, 8 genes in Drosophila, and 5 genes plus one truncated gene in Caenorhabditis elegans. Apart from the previously identified TALE classes MEIS, PBC, IRO, and TGIF, a novel class is identified, termed MOHAWK (MKX). Further, we show that the MEIS class can be divided into two families, PREP and MEIS. Prep genes have previously only been described in vertebrates but are lacking in Drosophila. Here we identify orthologues in other insect taxa as well as in the cnidarian Nematostella. In C. elegans, a divergent Prep protein has lost the homeodomain. Full-length multiple sequence alignment of the protostome and deuterostome sequences allowed us to identify several novel conserved motifs within the MKX, TGIF, and MEIS classes. Phylogenetic analyses revealed fast-evolving PBC class genes; in particular, some X-linked PBC genes in nematodes are subject to rapid evolution. In addition, several instances of gene loss were identified. In conclusion, our comprehensive analysis provides a defining framework for the classification of animal TALE homeobox genes and the understanding of their evolution.
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Affiliation(s)
- Krishanu Mukherjee
- Department of Biosciences and Nutrition, Karolinska Institutet, and School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
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Longhorn SJ, Foster PG, Vogler AP. The nematode?arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases. Cladistics 2007; 23:130-144. [DOI: 10.1111/j.1096-0031.2006.00132.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains. BMC Evol Biol 2007; 7:27. [PMID: 17319953 PMCID: PMC1810520 DOI: 10.1186/1471-2148-7-27] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 02/23/2007] [Indexed: 11/11/2022] Open
Abstract
Background Nuclear receptors (NRs) are important transcriptional modulators in metazoans which regulate transcription through binding to the promoter region of their target gene by the DNA binding domain (DBD) and activation or repression of mRNA synthesis through co-regulators bound to the ligand binding domain (LBD). NRs typically have a single DBD with a LBD. Results Three nuclear receptors named 2DBD-NRs, were identified from the flatworm Schistosoma mansoni that each possess a novel set of two DBDs in tandem with a LBD. They represent a novel NR modular structure: A/B-DBD-DBD-hinge-LBD. The 2DBD-NRs form a new subfamily of NRs, VII. By database mining, 2DBD-NR genes from other flatworm species (Schmidtea mediterranea and Dugesia japonica), from Mollusks (Lottia gigantean) and from arthropods (Daphnia pulex) were also identified. All 2DBD-NRs possess a P-box sequence of CEACKK in the first DBD, which is unique to 2DBD-NRs, and a P-box sequence of CEGCKG in the second DBD. Phylogenetic analyses of both DBD and ligand binding domain sequences showed that 2DBD-NR genes originate from a common two DBD-containing ancestor gene. A single 2DBD-NR orthologue was found in Arthropoda, Platyhelminths and Mollusca. Subsequent 2DBD-NR gene evolution in Mollusks and Platyhelminths involved gene duplication. Chromosome localization of S. mansoni 2DBD-NR genes by Fluorescent in situ hybridization (FISH) suggests that 2DBD-NR genes duplicated on different chromosomes in the Platyhelminths. Dimerization of Sm2DBDα indicates that 2DBD-NRs may act as homodimers, suggesting either that two repeats of a half-site are necessary for each DBD of 2DBD-NRs to bind to its target gene, or that each 2DBD-NR can recognize multiple sites. Conclusion 2DBD-NRs share a common ancestor gene which possessed an extra DBD that likely resulted from a recombination event. After the split of the Arthropods, Mollusks and Platyhelminths, 2DBD-NR underwent a recent duplication in a common ancestor of Mollusks, while two rounds of duplication occurred in a common ancestor of the Platyhelminths. This demonstrates that certain NR gene underwent recent duplication in Prostostome lineages after the split of the Prostostomia and Deuterostomia.
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Webster BL, Copley RR, Jenner RA, Mackenzie-Dodds JA, Bourlat SJ, Rota-Stabelli O, Littlewood DTJ, Telford MJ. Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan. Evol Dev 2006; 8:502-10. [PMID: 17073934 DOI: 10.1111/j.1525-142x.2006.00123.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Research into arthropod evolution is hampered by the derived nature and rapid evolution of the best-studied out-group: the nematodes. We consider priapulids as an alternative out-group. Priapulids are a small phylum of bottom-dwelling marine worms; their tubular body with spiny proboscis or introvert has changed little over 520 million years and recognizable priapulids are common among exceptionally preserved Cambrian fossils. Using the complete mitochondrial genome and 42 nuclear genes from Priapulus caudatus, we show that priapulids are slowly evolving ecdysozoans; almost all these priapulid genes have evolved more slowly than nematode orthologs and the priapulid mitochondrial gene order may be unchanged since the Cambrian. Considering their primitive bodyplan and embryology and the great conservation of both nuclear and mitochondrial genomes, priapulids may deserve the popular epithet of "living fossil." Their study is likely to yield significant new insights into the early evolution of the Ecdysozoa and the origins of the arthropods and their kin as well as aiding inference of the morphology of ancestral Ecdysozoa and Bilateria and their genomes.
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Affiliation(s)
- Bonnie L Webster
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Webster BL, Mackenzie-Dodds JA, Telford MJ, Littlewood DTJ. The mitochondrial genome of Priapulus caudatus Lamarck (Priapulida: Priapulidae). Gene 2006; 389:96-105. [PMID: 17123748 DOI: 10.1016/j.gene.2006.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 09/19/2006] [Accepted: 10/09/2006] [Indexed: 11/16/2022]
Abstract
We sequenced and annotated the complete mitochondrial (mt) genome of the priapulid Priapulus caudatus in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The genome was 14,919 bp in its entirety with few, short non-coding regions. A number of protein-coding and tRNA genes overlapped, making the genome relatively compact. The gene order was: cox1, cox2, trnK, trnD, atp8, atp6, cox3, trnG, nad3, trnA, trnR, trnN, rrnS, trnV, rrnL, trnL(yaa), trnL(nag), nad1, -trnS(nga), -cob, -nad6, trnP, -trnT, nad4L, nad4, trnH, nad5, trnF, -trnE, -trnS(nct), trnI, -trnQ, trnM, nad2, trnW, -trnC, -trnY; where '-' indicates genes transcribed on the opposite strand. The gene order, although unique amongst Metazoa, shared the greatest number of gene boundaries and the longest contiguous fragments with the chelicerate Limulus polyphemus. The mt genomes of these taxa differed only by a single inversion of 18 contiguous genes bounded by rrnS and trnS(nct). Other arthropods and nematodes shared fewer gene boundaries but considerably more than the most similar non-ecdysozoan.
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Affiliation(s)
- Bonnie L Webster
- Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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20
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Conway Morris S. Darwin's dilemma: the realities of the Cambrian 'explosion'. Philos Trans R Soc Lond B Biol Sci 2006; 361:1069-83. [PMID: 16754615 PMCID: PMC1578734 DOI: 10.1098/rstb.2006.1846] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Cambrian 'explosion' is widely regarded as one of the fulcrum points in the history of life, yet its origins and causes remain deeply controversial. New data from the fossil record, especially of Burgess Shale-type Lagerstätten, indicate, however, that the assembly of bodyplans is not only largely a Cambrian phenomenon, but can already be documented in fair detail. This speaks against a much more ancient origin of the metazoans, and current work is doing much to reconcile the apparent discrepancies between the fossil record, including the Ediacaran assemblages of latest Neoproterozoic age and molecular 'clocks'. Hypotheses to explain the Cambrian 'explosion' continue to be generated, but the recurrent confusion of cause and effect suggests that the wrong sort of question is being asked. Here I propose that despite its step-like function this evolutionary event is the inevitable consequence of Earth and biospheric change.
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Affiliation(s)
- Simon Conway Morris
- University of Cambridge, Department of Earth Sciences, Downing Street, Cambridge CB2 3EQ, UK.
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21
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Jager M, Quéinnec E, Houliston E, Manuel M. Expansion of the SOX gene family predated the emergence of the Bilateria. Mol Phylogenet Evol 2006; 39:468-77. [PMID: 16439161 DOI: 10.1016/j.ympev.2005.12.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 11/15/2005] [Accepted: 12/09/2005] [Indexed: 01/14/2023]
Abstract
Members of the SOX gene family are involved in regulating many developmental processes including neuronal determination and differentiation, and in carcinogenesis. So far they have only been identified in species from the Bilateria (deuterostomes and protostomes). To understand the origins of the SOX family, we used a PCR-based strategy to obtain 28 new sequences of SOX gene HMG domains from four non-bilaterian Metazoa: two sponge species, one ctenophore and one cnidarian. One additional SOX sequence was retrieved from EST sequences of the cnidarian species Clytia hemisphaerica. Unexpected SOX gene diversity was found in these species, especially in the cnidarian and the ctenophore. The topology of gene relationships deduced by Maximum Likelihood analysis, although not supported by bootstrap values, suggested that the SOX family started to diversify in the metazoan stem branch prior to the divergence of demosponges, and that further diversification occurred in the eumetazoan branch, as well as later in calcisponges, ctenophores, cnidarians and vertebrates. In contrast, gene loss appears to have occurred in the nematode and probably in other protostome lineages, explaining their lower number of SOX genes.
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Affiliation(s)
- Muriel Jager
- Equipe Evolution et Développement, UMR 7138 Systématique, Adaptation, Evolution CNRS/UMPC/MNHN/IRD/ENS Bâtiment B, 7ième étage, Université P et M Curie, 9 quai saint Bernard, 75005 Paris, France
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22
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Abstract
Two cannabinoid receptors, CB1 and CB2, are expressed in mammals, birds, reptiles, and fish. The presence of cannabinoid receptors in invertebrates has been controversial, due to conflicting evidence. We conducted a systematic review of the literature, using expanded search parameters. Evidence presented in the literature varied in validity, ranging from crude in vivo behavioural assays to robust in silico ortholog discovery. No research existed for several clades of invertebrates; we therefore tested for cannabinoid receptors in seven representative species, using tritiated ligand binding assays with [3H]CP55,940 displaced by the CB1-selective antagonist SR141716A. Specific binding of [3H]CP55,940 was found in neural membranes of Ciona intestinalis (Deuterstoma, a positive control), Lumbricusterrestris (Lophotrochozoa), and three ecdysozoans: Peripatoides novae-zealandiae (Onychophora), Jasus edwardi (Crustacea) and Panagrellus redivivus (Nematoda); the potency of displacement by SR141716A was comparable to measurements on rat cerebellum. No specific binding was observed in Actinothoe albocincta (Cnidaria) or Tethya aurantium (Porifera). The phylogenetic distribution of cannabinoid receptors may address taxonomic questions; previous studies suggested that the loss of CB1 was a synapomorphy shared by ecdysozoans. Our discovery of cannabinoid receptors in some nematodes, onychophorans, and crustaceans does not contradict the Ecdysozoa hypothesis, but gives it no support. We hypothesize that cannabinoid receptors evolved in the last common ancestor of bilaterians, with secondary loss occurring in insects and other clades. Conflicting data regarding Cnidarians precludes hypotheses regarding the last common ancestor of eumetazoans. No cannabinoid receptors are expressed in sponges, which probably diverged before the origin of the eumetazoan ancestor.
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23
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Lavrov DV, Lang BF. Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Syst Biol 2006; 54:651-9. [PMID: 16126659 DOI: 10.1080/10635150500221044] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Phylogenetic relationships among the metazoan phyla are the subject of an ongoing controversy. Analysis of mitochondrial gene arrangements is a powerful tool to investigate these relationships; however, its previous application outside of individual animal phyla has been hampered by the lack of informative out-group data. To address this shortcoming, we determined complete mitochondrial DNA sequences for the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. With sponges as an outgroup, we investigated phylogenetic relationships of nine bilaterian phyla using both breakpoint analysis of global mitochondrial gene arrangements and maximum parsimony analysis of mitochondrial gene adjacencies. Our results provide strong support for a group that includes protostome (but not deuterostome) coelomate, pseudocoelomate, and acoelomate animals, thus clearly rejecting the Coelomata hypothesis. Two other groups of bilaterian animals, Lophotrochozoa and Ambulacraria, are also supported by our analyses. However, due to the remarkable stability of mitochondrial gene arrangements in Deuterostomia and the Ecdysozoa, conclusions on their evolutionary history cannot be drawn.
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Affiliation(s)
- Dennis V Lavrov
- Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montreal, Que, H3C 3J7, Canada.
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24
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Dong XP, Donoghue PCJ, Cunningham JA, Liu JB, Cheng H. The anatomy, affinity, and phylogenetic significance of Markuelia. Evol Dev 2005; 7:468-82. [PMID: 16174039 DOI: 10.1111/j.1525-142x.2005.05050.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fossil record provides a paucity of data on the development of extinct organisms, particularly for their embryology. The recovery of fossilized embryos heralds new insight into the evolution of development but advances are limited by an almost complete absence of phylogenetic constraint. Markuelia is an exception to this, known from cleavage and pre-hatchling stages as a vermiform and profusely annulated direct-developing bilaterian with terminal circumoral and posterior radial arrays of spines. Phylogenetic analyses have hitherto suggested assignment to stem-Scalidophora (phyla Kinorhyncha, Loricifera, Priapulida). We test this assumption with additional data and through the inclusion of additional taxa. The available evidence supports stem-Scalidophora affinity, leading to the conclusion that scalidophorans, cyclonerualians, and ecdysozoans are primitive direct developers, and the likelihood that scalidophorans are primitively metameric.
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Affiliation(s)
- Xi-Ping Dong
- Department of Earth and Space Sciences, Peking University, Beijing 100871, China
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25
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Philippe H, Delsuc F, Brinkmann H, Lartillot N. Phylogenomics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2005. [DOI: 10.1146/annurev.ecolsys.35.112202.130205] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Frédéric Delsuc
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Henner Brinkmann
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Nicolas Lartillot
- Laboratoire d'Informatique, de Robotique et de Mathématiques de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, 34392 Montpellier Cedex 5, France;
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26
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Abstract
Renewed interest in the developmental basis of organismal complexity, and the emergence of new molecular tools, is improving our ability to study the evolution of metazoan body plans. The most substantial changes in body-plan organization occurred early in metazoan evolution; new model systems for studying basal metazoans are now being developed, and total-genome-sequencing initiatives are underway for at least three of the four most important taxa. The elucidation of how the gene networks that are involved in axial organization, germ-layer formation and cell differentiation are used differently during development is generating a more detailed understanding of the events that have led to the current diversity of multicellular life.
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Affiliation(s)
- Mark Q Martindale
- Kewalo Marine Laboratory, PBRC/University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA.
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27
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Abstract
MPhylogenetic analyses of hundreds of genes from model animals have placed flies closer to vertebrates than to nematodes; recent work suggests this may be due to an artefact known as long branch attraction.
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28
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29
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Steinauer ML, Nickol BB, Broughton R, Ortí G. First Sequenced Mitochondrial Genome from the Phylum Acanthocephala(Leptorhynchoides thecatus) and Its Phylogenetic Position Within Metazoa. J Mol Evol 2005; 60:706-15. [PMID: 15909226 DOI: 10.1007/s00239-004-0159-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 02/02/2005] [Indexed: 10/25/2022]
Abstract
The complete sequence of the mitochondrial genome of Leptorhynchoides thecatus (Acanthocephala) was determined, and a phylogenetic analysis was carried out to determine its placement within Metazoa. The genome is circular, 13,888 bp, and contains at least 36 of the 37 genes typically found in animal mitochondrial genomes. The genes for the large and small ribosomal RNA subunits are shorter than those of most metazoans, and the structures of most of the tRNA genes are atypical. There are two significant noncoding regions (377 and 294 bp), which are the best candidates for a control region; however, these regions do not appear similar to any of the control regions of other animals studied to date. The amino acid and nucleotide sequences of the protein coding genes of L. thecatus and 25 other metazoan taxa were used in both maximum likelihood and maximum parsimony phylogenetic analyses. Results indicate that among taxa with available mitochondrial genome sequences, Platyhelminthes is the closest relative to L. thecatus, which together are the sister taxon of Nematoda; however, long branches and/or base composition bias could be responsible for this result. The monophyly of Ecdysozoa, molting organisms, was not supported by any of the analyses. This study represents the first mitochondrial genome of an acanthocephalan to be sequenced and will allow further studies of systematics, population genetics, and genome evolution.
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Affiliation(s)
- Michelle L Steinauer
- Department of Biology, University of New Mexico, MSC 03 2020, 1 Univesity of New Mexico, Albuquerque, NM 87131-0001, USA.
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30
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Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005; 6:R41. [PMID: 15892869 PMCID: PMC1175953 DOI: 10.1186/gb-2005-6-5-r41] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 04/06/2005] [Indexed: 11/13/2022] Open
Abstract
The most extensive phylogenetic analysis carried out to date, including 11 complete genomes, is shown to support the Ecdysozoa hypothesis in the open-ended debate of the Coelomata-Ecdysozoa evolutionary problem. Background The issue of whether coelomates form a single clade, the Coelomata, or whether all animals that moult an exoskeleton (such as the coelomate arthropods and the pseudocoelomate nematodes) form a distinct clade, the Ecdysozoa, is the most puzzling issue in animal systematics and a major open-ended subject in evolutionary biology. Previous single-gene and genome-scale analyses designed to resolve the issue have produced contradictory results. Here we present the first genome-scale phylogenetic evidence that strongly supports the Ecdysozoa hypothesis. Results Through the most extensive phylogenetic analysis carried out to date, the complete genomes of 11 eukaryotic species have been analyzed in order to find homologous sequences derived from 18 human chromosomes. Phylogenetic analysis of datasets showing an increased adjustment to equal evolutionary rates between nematode and arthropod sequences produced a gradual change from support for Coelomata to support for Ecdysozoa. Transition between topologies occurred when fast-evolving sequences of Caenorhabditis elegans were removed. When chordate, nematode and arthropod sequences were constrained to fit equal evolutionary rates, the Ecdysozoa topology was statistically accepted whereas Coelomata was rejected. Conclusions The reliability of a monophyletic group clustering arthropods and nematodes was unequivocally accepted in datasets where traces of the long-branch attraction effect were removed. This is the first phylogenomic evidence to strongly support the 'moulting clade' hypothesis.
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Affiliation(s)
- Hernán Dopazo
- Pharmacogenomics and Comparative Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
| | - Joaquín Dopazo
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
- Functional Genomics Node, INB, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
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31
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Zdobnov EM, von Mering C, Letunic I, Bork P. Consistency of genome-based methods in measuring Metazoan evolution. FEBS Lett 2005; 579:3355-61. [PMID: 15943981 DOI: 10.1016/j.febslet.2005.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2005] [Indexed: 11/22/2022]
Abstract
Seven distinct genome-wide divergence measures were applied pairwise to the nine sequenced animal genomes of human, mouse, rat, chicken, pufferfish, fruit fly, mosquito, and two nematode worms (Caenorhabditis briggsae and Caenorhabditis elegans). Qualitatively, all of these divergence measures are found to correlate with the estimated time since speciation; however, marked deviations are observed in a few lineages. The distinct genome divergence measures also correlate well among themselves, indicating that most of the processes shaping genomes are dominated by neutral events. The deviations from the clock-like scenario in some lineages are observed consistently by several measures, implicitly confirming their reliability.
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32
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Rao AU, Carta LK, Lesuisse E, Hamza I. Lack of heme synthesis in a free-living eukaryote. Proc Natl Acad Sci U S A 2005; 102:4270-5. [PMID: 15767563 PMCID: PMC555530 DOI: 10.1073/pnas.0500877102] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Indexed: 11/18/2022] Open
Abstract
In most free-living eukaryotes studied thus far, heme is synthesized from a series of intermediates through a well defined evolutionarily conserved pathway. We found that free-living worms, including the model genetic organism Caenorhabditis elegans, and parasitic helminths are unable to synthesize heme de novo, even though these animals contain hemoproteins that function in key biological processes. Radioisotope, fluorescence labeling, and heme analog studies suggest that C. elegans acquires heme from exogenous sources. Iron-deprived worms were unable to grow in the presence of adequate heme unless rescued by increasing heme levels in the growth medium. These data indicate that although worms use dietary heme for incorporation into hemoproteins, ingested heme is also used as an iron source when iron is limiting. Our results provide a biochemical basis for the dependence of worm growth and development on heme, and they suggest that pharmacologic targeting of heme transport pathways in worms could be an important control measure for helminthic infections.
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Affiliation(s)
- Anita U Rao
- Department of Animal and Avian Sciences and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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33
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Blair JE, Shah P, Hedges SB. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics 2005; 6:53. [PMID: 15762985 PMCID: PMC1274250 DOI: 10.1186/1471-2105-6-53] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 03/11/2005] [Indexed: 11/29/2022] Open
Abstract
Background Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. Results Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. Conclusion Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes.
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Affiliation(s)
- Jaime E Blair
- NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, Pennsylvania 16802-5301, USA
| | - Prachi Shah
- NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, Pennsylvania 16802-5301, USA
| | - S Blair Hedges
- NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, Pennsylvania 16802-5301, USA
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34
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Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 2005; 22:1246-53. [PMID: 15703236 DOI: 10.1093/molbev/msi111] [Citation(s) in RCA: 354] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). However, it received little additional support. In fact, several multigene analyses strongly argued against this new phylogeny. These latter studies were based on a large amount of sequence data and therefore showed an apparently strong statistical support. Yet, they covered only a few taxa (those for which complete genomes were available), making systematic artifacts of tree reconstruction more probable. Here we expand this sparse taxonomic sampling and analyze a large data set (146 genes, 35,371 positions) from a diverse sample of animals (35 species). Our study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies. A refined analysis of our data set excluding the most biased genes provides strong support in favor of the new animal phylogeny and in addition suggests that urochordates are more closely related to vertebrates than are cephalochordates. These findings have important implications for the interpretation of morphological and genomic data.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research and Département de Biochimie, Université de Montréal, Montréal, Québec, Canada.
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Philip GK, Creevey CJ, McInerney JO. The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa. Mol Biol Evol 2005; 22:1175-84. [PMID: 15703245 DOI: 10.1093/molbev/msi102] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In considering the best possible solutions for answering phylogenetic questions from genomic sequences, we have chosen a strategy that we suggest is superior to others that have gone previously. We have ignored multigene families and instead have used single-gene families. This minimizes the inadvertent analysis of paralogs. We have employed strict data controls and have reasoned that if a protein is not capable of recovering the uncontroversial parts of a phylogenetic tree, then why should we use it for the more controversial parts? We have sliced and diced the data in as many ways as possible in order to uncover the signals in that data. Using this strategy, we have tested two controversial hypotheses concerning eukaryotic phylogenetic relationships: the placement of arthropoda and nematodes and the relationships of animals, plants, and fungi. We have constructed phylogenetic trees from 780 single-gene families from 10 completed genomes and amalgamated these into a single supertree. We have also carried out a total evidence analysis on the only universally distributed protein families that can accurately reconstruct the uncontroversial parts of the phylogenetic tree: a total of five families. In doing so, we ignore the majority of single-gene families that are universally distributed as they do not have the appropriate signals to recover the uncontroversial parts of the tree. We have also ignored every protein that has ever been used previously to address this issue, simply because none of them meet our strict criteria. Using these data controls, site stripping, and multiple analyses, 24 out of 26 analyses strongly support the grouping of vertebrates with arthropods (Coelomata hypothesis) and plants with animals. In the other two analyses, the data were ambivalent. The latter finding overturns an 11-year theory of Eukaryotic evolution; the first confirms what has already been said by others. In the light of this new tree, we re-analyze the evolution of intron gain and loss in the rpL14 gene and find that it is much more compatible with the hypothesis presented here than with the Opisthokonta hypothesis.
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Affiliation(s)
- Gayle K Philip
- Department of Biology, National University of Ireland Maynooth, Co. Kildare, Ireland
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Nicholson AC, Malik SB, Logsdon JM, Van Meir EG. Functional evolution of ADAMTS genes: evidence from analyses of phylogeny and gene organization. BMC Evol Biol 2005; 5:11. [PMID: 15693998 PMCID: PMC549037 DOI: 10.1186/1471-2148-5-11] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Accepted: 02/04/2005] [Indexed: 11/21/2022] Open
Abstract
Background The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs) proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs) common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10), thrombotic thrombocytopenic purpura (ADAMTS13), and Ehlers-Danlos syndrome type VIIC (ADAMTS2) in humans and belted white-spotting mutation in mice (ADAMTS20). Results Phylogenetic analysis and comparison of the exon/intron organization of vertebrate (Homo, Mus, Fugu), chordate (Ciona) and invertebrate (Drosophila and Caenorhabditis) ADAMTS homologs has elucidated the evolutionary relationships of this important gene family, which comprises 19 members in humans. Conclusions The evolutionary history of ADAMTS genes in vertebrate genomes has been marked by rampant gene duplication, including a retrotransposition that gave rise to a distinct ADAMTS subfamily (ADAMTS1, -4, -5, -8, -15) that may have distinct aggrecanase and angiogenesis functions.
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Affiliation(s)
- Ainsley C Nicholson
- Laboratory of Molecular Neuro-Oncology, Neurosurgery Department and Winship Cancer Institute, 1365-C Clifton Road, Room C5078, Emory University, Atlanta GA 30322 USA
| | - Shehre-Banoo Malik
- Roy J. Carver Center for Comparative Genomics, Department of Biological Sciences, 300 Old Biology Building, University of Iowa, Iowa City IA 52242-1324 USA
| | - John M Logsdon
- Roy J. Carver Center for Comparative Genomics, Department of Biological Sciences, 300 Old Biology Building, University of Iowa, Iowa City IA 52242-1324 USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Neurosurgery Department and Winship Cancer Institute, 1365-C Clifton Road, Room C5078, Emory University, Atlanta GA 30322 USA
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Abstract
MOTIVATION In this paper, we shall examine the evolution of domain architectures across 62 genomes of known phylogeny including all kingdoms of life. We look in particular at the possibility of convergent evolution, with a view to determining the extent to which the architectures observed in the genomes are due to functional necessity or evolutionary descent. We used domains of known structure, because from this and other information we know their evolutionary relationships. We use a range of methods including phylogenetic grouping, sequence similarity/alignment, mutation rates and comparative genomics to approach this difficult problem from several angles. RESULTS Although we do not claim an exhaustive analysis, we conclude that between 0.4 and 4% of sequences are involved in convergent evolution of domain architectures, and expect the actual number to be close to the lower bound. We also made two incidental observations, albeit on a small sample: the events leading to convergent evolution appear to be random with no functional or structural preferences, and changes in the number of tandem repeat domains occur more readily than changes which alter the domain composition. CONCLUSION The principal conclusion is that the observed domain architectures of the sequences in the genomes are driven by evolutionary descent rather than functional necessity. CONTACT gough@supfam.org.
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Affiliation(s)
- Julian Gough
- RIKEN Genomic Sciences Centre, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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Abstract
Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.
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Affiliation(s)
- Henry N Higgs
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA.
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