1
|
Ma L, Liu Q, Wei S, Liu S, Tian L, Song F, Duan Y, Cai W, Li H. Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus (Thysanoptera: Thripidae). Sci Data 2023; 10:252. [PMID: 37137922 PMCID: PMC10156705 DOI: 10.1038/s41597-023-02164-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Bean flower thrips Megalurothrips usitatus is a staple pest of cowpea and other legumes and causes dramatic economic losses. Its small size allows for easy concealment, and large reproductive capacity easily leads to infestations. Despite the importance of a genome in developing novel management strategies, genetic studies on M. usitatus remain limited. Thus, we generated a chromosome-level M. usitatus genome using a combination of PacBio long read and Hi-C technologies. The assembled genome was 238.14 Mb with a scaffold N50 of 13.85 Mb. The final genome was anchored into 16 pseudo-chromosomes containing 14,000 genes, of which 91.74% were functionally annotated. Comparative genomic analyses revealed that expanded gene families were enriched in fatty acid metabolism and detoxification metabolism (ABC transporters), and contracted gene families were strongly associated with chitin-based cuticle development and sensory perception of taste. In conclusion, this high-quality genome provides an invaluable resource for us to understand the thrips' ecology and genetics, contributing to pest management.
Collapse
Affiliation(s)
- Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Shujun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| |
Collapse
|
2
|
Aydemir MN, Aydemir HB, Budak M, Kızıltepe B, Çelebi MŞ, Korkmaz EM, Başıbüyük HH. A novel, conserved and possibly functional motif "WHWGHTW" in mitochondrial transcription across Bilateria. Mitochondrion 2023; 68:72-80. [PMID: 36400160 DOI: 10.1016/j.mito.2022.11.004] [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: 03/22/2022] [Revised: 08/22/2022] [Accepted: 11/05/2022] [Indexed: 11/17/2022]
Abstract
The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of 'WWWGHTW' were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.
Collapse
Affiliation(s)
- Merve Nur Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey.
| | - Habeş Bilal Aydemir
- Tokat Gaziosmanpaşa University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 60250 Tokat, Turkey
| | - Mahir Budak
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Birsel Kızıltepe
- Sivas Cumhuriyet University, Graduate School of Natural and Applied Sciences, Department of Bioinformatics, 58140 Sivas, Turkey
| | - Melissa Şafak Çelebi
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Ertan Mahir Korkmaz
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, 58140 Sivas, Turkey
| | - Hasan Hüseyin Başıbüyük
- Akdeniz University, Faculty of Health Sciences, Department of Gerontology, 07070 Antalya, Turkey
| |
Collapse
|
3
|
Schachat SR, Goldstein PZ, Desalle R, Bobo DM, Boyce CK, Payne JL, Labandeira CC. Illusion of flight? Absence, evidence and the age of winged insects. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.
Collapse
Affiliation(s)
- Sandra R Schachat
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Paul Z Goldstein
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Rob Desalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
| | - Dean M Bobo
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University , New York, NY , USA
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Jonathan L Payne
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Conrad C Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Entomology and Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park , MD , USA
- Capital Normal University, School of Life Sciences , Beijing , China
| |
Collapse
|
4
|
Martin C, Jahn H, Klein M, Hammel JU, Stevenson PA, Homberg U, Mayer G. The velvet worm brain unveils homologies and evolutionary novelties across panarthropods. BMC Biol 2022; 20:26. [PMID: 35073910 PMCID: PMC9136957 DOI: 10.1186/s12915-021-01196-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of the brain and its major neuropils in Panarthropoda (comprising Arthropoda, Tardigrada and Onychophora) remains enigmatic. As one of the closest relatives of arthropods, onychophorans are regarded as indispensable for a broad understanding of the evolution of panarthropod organ systems, including the brain, whose anatomical and functional organisation is often used to gain insights into evolutionary relations. However, while numerous recent studies have clarified the organisation of many arthropod nervous systems, a detailed investigation of the onychophoran brain with current state-of-the-art approaches is lacking, and further inconsistencies in nomenclature and interpretation hamper its understanding. To clarify the origins and homology of cerebral structures across panarthropods, we analysed the brain architecture in the onychophoran Euperipatoides rowelli by combining X-ray micro-computed tomography, histology, immunohistochemistry, confocal microscopy, and three-dimensional reconstruction. RESULTS Here, we use this detailed information to generate a consistent glossary for neuroanatomical studies of Onychophora. In addition, we report novel cerebral structures, provide novel details on previously known brain areas, and characterise further structures and neuropils in order to improve the reproducibility of neuroanatomical observations. Our findings support homology of mushroom bodies and central bodies in onychophorans and arthropods. Their antennal nerve cords and olfactory lobes most likely evolved independently. In contrast to previous reports, we found no evidence for second-order visual neuropils, or a frontal ganglion in the velvet worm brain. CONCLUSION We imaged the velvet worm nervous system at an unprecedented level of detail and compiled a comprehensive glossary of known and previously uncharacterised neuroanatomical structures to provide an in-depth characterisation of the onychophoran brain architecture. We expect that our data will improve the reproducibility and comparability of future neuroanatomical studies.
Collapse
Affiliation(s)
- Christine Martin
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany.
| | - Henry Jahn
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany
| | - Mercedes Klein
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany
| | - Jörg U Hammel
- Institute of Materials Physics, Helmholtz-Zentrum hereon, 21502, Geesthacht, Germany
| | - Paul A Stevenson
- Physiology of Animals and Behaviour, Institute of Biology, University of Leipzig, 04103, Leipzig, Germany
| | - Uwe Homberg
- Department of Biology, Animal Physiology, Philipps-Universität Marburg, 35043, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus Liebig University Giessen, 35032, Marburg, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany.
| |
Collapse
|
5
|
The mitochondrial aspartate/glutamate carrier (AGC or Aralar1) isoforms in D. melanogaster: biochemical characterization, gene structure, and evolutionary analysis. Biochim Biophys Acta Gen Subj 2021; 1865:129854. [PMID: 33497735 DOI: 10.1016/j.bbagen.2021.129854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND In man two mitochondrial aspartate/glutamate carrier (AGC) isoforms, known as aralar and citrin, are required to accomplish several metabolic pathways. In order to fill the existing gap of knowledge in Drosophila melanogaster, we have studied aralar1 gene, orthologue of human AGC-encoding genes in this organism. METHODS The blastp algorithm and the "reciprocal best hit" approach have been used to identify the human orthologue of AGCs in Drosophilidae and non-Drosophilidae. Aralar1 proteins have been overexpressed in Escherichia coli and functionally reconstituted into liposomes for transport assays. RESULTS The transcriptional organization of aralar1 comprises six isoforms, three constitutively expressed (aralar1-RA, RD and RF), and the remaining three distributed during the development or in different tissues (aralar1-RB, RC and RE). Aralar1-PA and Aralar1-PE, representative of all isoforms, have been biochemically characterized. Recombinant Aralar1-PA and Aralar1-PE proteins share similar efficiency to exchange glutamate against aspartate, and same substrate affinities than the human isoforms. Interestingly, although Aralar1-PA and Aralar1-PE diverge only in their EF-hand 8, they greatly differ in their specific activities and substrate specificity. CONCLUSIONS The tight regulation of aralar1 transcripts expression and the high request of aspartate and glutamate during early embryogenesis suggest a crucial role of Aralar1 in this Drosophila developmental stage. Furthermore, biochemical characterization and calcium sensitivity have identified Aralar1-PA and Aralar1-PE as the human aralar and citrin counterparts, respectively. GENERAL SIGNIFICANCE The functional characterization of the fruit fly mitochondrial AGC transporter represents a crucial step toward a complete understanding of the metabolic events acting during early embryogenesis.
Collapse
|
6
|
Jeong JH, Kim H, Ryu S, Kim W. The First Pycnogonid Draft Genome of Nymphon striatum. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.554164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
7
|
Edgecombe GD. Arthropod Origins: Integrating Paleontological and Molecular Evidence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124437] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history.
Collapse
Affiliation(s)
- Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| |
Collapse
|
8
|
Dunoyer LA, Seifert AW, Van Cleve J. Evolutionary bedfellows: Reconstructing the ancestral state of autotomy and regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:94-115. [PMID: 32558244 DOI: 10.1002/jez.b.22974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 11/11/2022]
Abstract
Some form of regeneration occurs in all lifeforms and extends from single-cell organisms to humans. The degree to which regenerative ability is distributed across different taxa, however, is harder to ascertain given the potential for phylogenetic constraint or inertia, and adaptive processes to shape this pattern. Here, we examine the phylogenetic history of regeneration in two groups where the trait has been well-studied: arthropods and reptiles. Because autotomy is often present alongside regeneration in these groups, we performed ancestral state reconstructions for both traits to more precisely assess the timing of their origins and the degree to which these traits coevolve. Using an ancestral trait reconstruction, we find that autotomy and regeneration were present at the base of the arthropod and reptile trees. We also find that when autotomy is lost it does not re-evolve easily. Lastly, we find that the distribution of regeneration is intimately connected to autotomy with the association being stronger in reptiles than in arthropods. Although these patterns suggest that decoupling autotomy and regeneration at a broad phylogenetic scale may be difficult, the available data provides useful insight into their entanglement. Ultimately, our reconstructions provide the important groundwork to explore how selection may have played a role during the loss of regeneration in specific lineages.
Collapse
Affiliation(s)
- Luc A Dunoyer
- Department of Biology, University of Kentucky, Lexington, Kentucky.,Department of Life Sciences, Wake Technical Community College, Raleigh, North Carolina
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
9
|
Montagna M, Tong KJ, Magoga G, Strada L, Tintori A, Ho SYW, Lo N. Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proc Biol Sci 2019; 286:20191854. [PMID: 31594499 PMCID: PMC6790769 DOI: 10.1098/rspb.2019.1854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
Collapse
Affiliation(s)
- Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - K. Jun Tong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Laura Strada
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Andrea Tintori
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| |
Collapse
|
10
|
Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090169] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity.
Collapse
|
11
|
Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
Collapse
Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
12
|
p47 licenses activation of the immune deficiency pathway in the tick Ixodes scapularis. Proc Natl Acad Sci U S A 2018; 116:205-210. [PMID: 30559180 DOI: 10.1073/pnas.1808905116] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The E3 ubiquitin ligase X-linked inhibitor of apoptosis (XIAP) acts as a molecular rheostat for the immune deficiency (IMD) pathway of the tick Ixodes scapularis How XIAP activates the IMD pathway in response to microbial infection remains ill defined. Here, we identified the XIAP enzymatic substrate p47 as a positive regulator of the I. scapularis IMD network. XIAP polyubiquitylates p47 in a lysine 63-dependent manner and interacts with the p47 ubiquitin-like (UBX) module. p47 also binds to Kenny (IKKγ/NEMO), the regulatory subunit of the inhibitor of nuclear factor (NF)- κB kinase complex. Replacement of the amino acid lysine to arginine within the p47 linker region completely abrogated molecular interactions with Kenny. Furthermore, mitigation of p47 transcription levels through RNA interference in I. scapularis limited Kenny accumulation, reduced phosphorylation of IKKβ (IRD5), and impaired cleavage of the NF-κB molecule Relish. Accordingly, disruption of p47 expression increased microbial colonization by the Lyme disease spirochete Borrelia burgdorferi and the rickettsial agent Anaplasma phagocytophilum Collectively, we highlight the importance of ticks for the elucidation of paradigms in arthropod immunology. Manipulating immune signaling cascades within I. scapularis may lead to innovative approaches to reducing the burden of tick-borne diseases.
Collapse
|
13
|
Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
Collapse
|
14
|
Scherbaum S, Hellmann N, Fernández R, Pick C, Burmester T. Diversity, evolution, and function of myriapod hemocyanins. BMC Evol Biol 2018; 18:107. [PMID: 29976142 PMCID: PMC6034248 DOI: 10.1186/s12862-018-1221-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 06/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background Hemocyanin transports O2 in the hemolymph of many arthropod species. Such respiratory proteins have long been considered unnecessary in Myriapoda. As a result, the presence of hemocyanin in Myriapoda has long been overlooked. We analyzed transcriptome and genome sequences from all major myriapod taxa – Chilopoda, Diplopoda, Symphyla, and Pauropoda – with the aim of identifying hemocyanin-like proteins. Results We investigated the genomes and transcriptomes of 56 myriapod species and identified 46 novel full-length hemocyanin subunit sequences in 20 species of Chilopoda, Diplopoda, and Symphyla, but not Pauropoda. We found in Cleidogona sp. (Diplopoda, Chordeumatida) a hemocyanin-like sequence with mutated copper-binding centers, which cannot bind O2. An RNA-seq approach showed markedly different hemocyanin mRNA levels from ~ 6 to 25,000 reads per kilobase per million reads. To evaluate the contribution of hemocyanin to O2 transport, we specifically studied the hemocyanin of the centipede Scolopendra dehaani. This species harbors two distinct hemocyanin subunits with low expression levels. We showed cooperative O2 binding in the S. dehaani hemolymph, indicating that hemocyanin supports O2 transport even at low concentration. Further, we demonstrated that hemocyanin is > 1500-fold more highly expressed in the fertilized egg than in the adult. Conclusion Hemocyanin was most likely the respiratory protein in the myriapod stem-lineage, but multiple taxa may have independently lost hemocyanin and thus the ability of efficient O2 transport. In myriapods, hemocyanin is much more widespread than initially appreciated. Some myriapods express hemocyanin only at low levels, which are, nevertheless, sufficient for O2 supply. Notably, also in myriapods, a non-respiratory protein similar to insect storage hexamerins evolved from the hemocyanin. Electronic supplementary material The online version of this article (10.1186/s12862-018-1221-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Nadja Hellmann
- Institute for Biophysics, Johannes Gutenberg University of Mainz, D-55099, Mainz, Germany
| | - Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.,Bioinformatics & Genomics Unit, Center for Genomic Regulation, 08004, Barcelona, Spain
| | - Christian Pick
- Institute of Zoology, University of Hamburg, D-20146, Hamburg, Germany
| | | |
Collapse
|
15
|
Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP. A phylogenomic framework and timescale for comparative studies of tunicates. BMC Biol 2018; 16:39. [PMID: 29653534 PMCID: PMC5899321 DOI: 10.1186/s12915-018-0499-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/13/2023] Open
Abstract
Background Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species. Results Phylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~ 450–350 million years ago) among the major groups and allow one to compare their evolutionary age with respect to the major vertebrate model lineages. Conclusions Our study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies. Electronic supplementary material The online version of this article (10.1186/s12915-018-0499-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station d'Ecologie Théorique et Expérimentale, Moulis, France.,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Canada
| | - Georgia Tsagkogeorga
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Marie-Ka Tilak
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB, CSIC), Girona, Spain
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Jacques Piette
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université de Montpellier, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université de Montpellier, Montpellier, France
| | | |
Collapse
|
16
|
|
17
|
Abstract
The discovery of fossilized brains and ventral nerve cords in lower and mid-Cambrian arthropods has led to crucial insights about the evolution of their central nervous system, the segmental identity of head appendages and the early evolution of eyes and their underlying visual systems. Fundamental ground patterns of lower Cambrian arthropod brains and nervous systems correspond to the ground patterns of brains and nervous systems belonging to three of four major extant panarthropod lineages. These findings demonstrate the evolutionary stability of early neural arrangements over an immense time span. Here, we put these fossil discoveries in the context of evidence from cladistics, as well as developmental and comparative neuroanatomy, which together suggest that despite many evolved modifications of neuropil centers within arthropod brains and ganglia, highly conserved arrangements have been retained. Recent phylogenies of the arthropods, based on fossil and molecular evidence, and estimates of divergence dates, suggest that neural ground patterns characterizing onychophorans, chelicerates and mandibulates are likely to have diverged between the terminal Ediacaran and earliest Cambrian, heralding the exuberant diversification of body forms that account for the Cambrian Explosion.
Collapse
Affiliation(s)
- Nicholas J Strausfeld
- Department of Neuroscience and Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
| | - Xiaoya Ma
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, People's Republic of China
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| |
Collapse
|
18
|
Phylogeny mandalas for illustrating the Tree of Life. Mol Phylogenet Evol 2017; 117:168-178. [DOI: 10.1016/j.ympev.2016.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
|
19
|
Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex. Genetics 2017; 207:697-710. [PMID: 28811387 DOI: 10.1534/genetics.117.300146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/11/2017] [Indexed: 12/26/2022] Open
Abstract
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here, we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex, in addition to six isolates from a non-MA population originating from the same progenitor, to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual repeats were both high and highly variable, ranging from additions/deletions of 0.29-105 copies per generation (reflecting changes of 0.12-0.80% per generation). Our results also provide evidence that new repeat sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33% lower variation in repeat copy number on average than the MA lines, although the level of selective constraint was not evenly distributed across all repeats. The changes between many pairs of repeats were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that tandem repeats can experience extremely rapid evolution in copy number, which can lead to high levels of divergence in genome-wide repeat composition between closely related species.
Collapse
|
20
|
Martin C, Gross V, Hering L, Tepper B, Jahn H, de Sena Oliveira I, Stevenson PA, Mayer G. The nervous and visual systems of onychophorans and tardigrades: learning about arthropod evolution from their closest relatives. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 203:565-590. [DOI: 10.1007/s00359-017-1186-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/02/2017] [Accepted: 05/29/2017] [Indexed: 12/19/2022]
|
21
|
Satler JD, Carstens BC. Do ecological communities disperse across biogeographic barriers as a unit? Mol Ecol 2017; 26:3533-3545. [DOI: 10.1111/mec.14137] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 03/13/2017] [Accepted: 03/29/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jordan D. Satler
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
| |
Collapse
|
22
|
Chipman AD. Oncopeltus fasciatus
as an evo-devo research organism. Genesis 2017; 55. [DOI: 10.1002/dvg.23020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/29/2016] [Accepted: 01/15/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ariel D. Chipman
- The Department of Ecology; Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus; Givat Ram Jerusalem 91904 Israel
| |
Collapse
|
23
|
Comparative genomics provides a timeframe for Wolbachia evolution and exposes a recent biotin synthesis operon transfer. Nat Microbiol 2016; 2:16241. [PMID: 28005061 DOI: 10.1038/nmicrobiol.2016.241] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/29/2016] [Indexed: 11/08/2022]
Abstract
The genus Wolbachia (Alphaproteobacteria) comprises the most abundant inherited intracellular bacteria1. Despite their relevance as manipulators of human pathogen transmission2 and arthropod reproduction3, many aspects of their evolutionary history are not well understood4. In arthropods, Wolbachia infections are typically transient on evolutionary timescales5,6 and co-divergence between hosts and Wolbachia is supposedly rare. Consequently, much of our knowledge of Wolbachia genome evolution derives from very recently diverged strains, and a timescale for Wolbachia is lacking. Here, we investigated the genomes of four Wolbachia strains that have persisted within and co-diverged with their host lineage for ∼2 million years. Although the genomes showed very little evolutionary change on a nucleotide level, we found evidence for a recent lateral transfer of a complete biotin synthesis operon that has the potential to transform Wolbachia-host relationships7. Furthermore, this evolutionary snapshot enabled us to calibrate the divergence times of the supergroup A and B Wolbachia lineages using genome-wide data sets and relaxed molecular clock models. We estimated the origin of Wolbachia supergroups A and B to be ∼200 million years ago (Ma), which is considerably older than previously appreciated. This age coincides with the diversification of many insect lineages8 that represent most of Wolbachia's host spectrum.
Collapse
|
24
|
Wang YH, Engel MS, Rafael JA, Wu HY, Rédei D, Xie Q, Wang G, Liu XG, Bu WJ. Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda). Sci Rep 2016; 6:38939. [PMID: 27958352 PMCID: PMC5154178 DOI: 10.1038/srep38939] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 11/16/2016] [Indexed: 11/08/2022] Open
Abstract
Insecta s. str. (=Ectognatha), comprise the largest and most diversified group of living organisms, accounting for roughly half of the biodiversity on Earth. Understanding insect relationships and the specific time intervals for their episodes of radiation and extinction are critical to any comprehensive perspective on evolutionary events. Although some deeper nodes have been resolved congruently, the complete evolution of insects has remained obscure due to the lack of direct fossil evidence. Besides, various evolutionary phases of insects and the corresponding driving forces of diversification remain to be recognized. In this study, a comprehensive sample of all insect orders was used to reconstruct their phylogenetic relationships and estimate deep divergences. The phylogenetic relationships of insect orders were congruently recovered by Bayesian inference and maximum likelihood analyses. A complete timescale of divergences based on an uncorrelated log-normal relaxed clock model was established among all lineages of winged insects. The inferred timescale for various nodes are congruent with major historical events including the increase of atmospheric oxygen in the Late Silurian and earliest Devonian, the radiation of vascular plants in the Devonian, and with the available fossil record of the stem groups to various insect lineages in the Devonian and Carboniferous.
Collapse
Affiliation(s)
- Yan-hui Wang
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, 1501 Crestline Drive – Suite 140, University of Kansas, Lawrence, Kansas 66045, USA
| | - José A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Caixa Postal 478, 69011-970 Manaus, Amazonas, Brazil
| | - Hao-yang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Dávid Rédei
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Gang Wang
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
| | - Xiao-guang Liu
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
| | - Wen-jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| |
Collapse
|
25
|
Fernández R, Edgecombe GD, Giribet G. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Syst Biol 2016; 65:871-89. [PMID: 27162151 PMCID: PMC4997009 DOI: 10.1093/sysbio/syw041] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/28/2016] [Indexed: 11/14/2022] Open
Abstract
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
Collapse
Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| |
Collapse
|
26
|
Ješovnik A, González VL, Schultz TR. Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma. PLoS One 2016; 11:e0151059. [PMID: 27466804 PMCID: PMC4965065 DOI: 10.1371/journal.pone.0151059] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/22/2016] [Indexed: 01/27/2023] Open
Abstract
Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus Sericomyrmex and a single lower-attine ant species, Apterostigma megacephala, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee Apis mellifera for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6-66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus Sericomyrmex. This result is further confirmed by a separate analysis of the three Sericomyrmex species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly argininosuccinate synthase and argininosuccinate lyase, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for Sericomyrmex species, the absence of arginine anabolic genes in the lower-attine ant Apterostigma megacephala strongly suggests that the loss coincided with the origin of attine ants.
Collapse
Affiliation(s)
- Ana Ješovnik
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
- Maryland Center for Systematic Entomology, Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Vanessa L. González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Ted R. Schultz
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| |
Collapse
|
27
|
Lozano-Fernandez J, Carton R, Tanner AR, Puttick MN, Blaxter M, Vinther J, Olesen J, Giribet G, Edgecombe GD, Pisani D. A molecular palaeobiological exploration of arthropod terrestrialization. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150133. [PMID: 27325830 PMCID: PMC4920334 DOI: 10.1098/rstb.2015.0133] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/28/2022] Open
Abstract
Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
Collapse
Affiliation(s)
- Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Robert Carton
- Department of Biology, The National University of Ireland Maynooth, Maynooth, Kildare, Ireland
| | - Alastair R Tanner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3TF, UK
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
28
|
Havird JC, Santos SR. Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015. Integr Comp Biol 2016; 56:1055-1066. [PMID: 27400974 DOI: 10.1093/icb/icw061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Despite their economic, ecological, and experimental importance, genomic resources remain scarce for crustaceans. In lieu of genomes, many researchers have taken advantage of technological advancements to instead sequence and assemble crustacean transcriptomes de novo However, there is little consensus on what standard operating procedures are, or should be, for the field. Here, we systematically reviewed 53 studies published during 2014-2015 that utilized transcriptomic resources from this taxonomic group in an effort to identify commonalities as well as potential weaknesses that have applicability beyond just crustaceans. In general, these studies utilized RNA-Seq data, both novel and publicly available, to characterize transcriptomes and/or identify differentially expressed genes (DEGs) between treatments. Although the software suite Trinity was popular in assembly pipelines and other programs were also commonly employed, many studies failed to report crucial details regarding bioinformatic methodologies, including read mappers and the utilized parameters in identifying and characterizing DEGs. Annotation percentages for assembled transcriptomic contigs were low, averaging 32% overall. While other metrics, such as numbers of contigs and DEGs reported, correlated with the number of sequence reads utilized per sample, these did reach apparent saturation with increasing sequencing depth. Most disturbingly, a number of studies (55%) reported DEGs based on non-replicated experimental designs and single biological replicates for each treatment. Given this, we suggest future RNA-Seq experiments targeting transcriptome characterization conduct deeper (i.e., 50-100 M reads) sequencing while those examining differential expression instead focus more on increased biological replicates at shallower (i.e., ∼10-20 M reads/sample) sequencing depths. Moreover, the community must avoid submitting for review, or accepting for publication, non-replicated differential expression studies. Finally, mining the ever growing publicly available transcriptomic data from crustaceans will allow future studies to focus on hypothesis-driven research instead of continuing to simply characterize transcriptomes. As an example of this, we utilized neurotoxin sequences from the recently described remipede venom gland transcriptome in conjunction with publicly available crustacean transcriptomic data to derive preliminary results and hypotheses regarding the evolution of venom in crustaceans.
Collapse
Affiliation(s)
- Justin C Havird
- *Department of Biology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Scott R Santos
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg, Auburn, AL 36849, USA
| |
Collapse
|
29
|
Two temporal functions of Glass: Ommatidium patterning and photoreceptor differentiation. Dev Biol 2016; 414:4-20. [PMID: 27105580 DOI: 10.1016/j.ydbio.2016.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/04/2016] [Accepted: 04/13/2016] [Indexed: 12/28/2022]
Abstract
Much progress has been made in elucidating the molecular networks required for specifying retinal cells, including photoreceptors, but the downstream mechanisms that maintain identity and regulate differentiation remain poorly understood. Here, we report that the transcription factor Glass has a dual role in establishing a functional Drosophila eye. Utilizing conditional rescue approaches, we confirm that persistent defects in ommatidium patterning combined with cell death correlate with the overall disruption of eye morphology in glass mutants. In addition, we reveal that Glass exhibits a separable role in regulating photoreceptor differentiation. In particular, we demonstrate the apparent loss of glass mutant photoreceptors is not only due to cell death but also a failure of the surviving photoreceptors to complete differentiation. Moreover, the late reintroduction of Glass in these developmentally stalled photoreceptors is capable of restoring differentiation in the absence of correct ommatidium patterning. Mechanistically, transcription profiling at the time of differentiation reveals that Glass is necessary for the expression of many genes implicated in differentiation, i.e. rhabdomere morphogenesis, phototransduction, and synaptogenesis. Specifically, we show Glass directly regulates the expression of Pph13, which encodes a transcription factor necessary for opsin expression and rhabdomere morphogenesis. Finally, we demonstrate the ability of Glass to choreograph photoreceptor differentiation is conserved between Drosophila and Tribolium, two holometabolous insects. Altogether, our work identifies a fundamental regulatory mechanism to generate the full complement of cells required for a functional rhabdomeric visual system and provides a critical framework to investigate the basis of differentiation and maintenance of photoreceptor identity.
Collapse
|
30
|
Letsch H, Gottsberger B, Ware JL. Not going with the flow: a comprehensive time-calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification. Mol Ecol 2016; 25:1340-53. [DOI: 10.1111/mec.13562] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Harald Letsch
- Department für Botanik und Biodiversitätsforschung; Universität Wien; Rennweg 14 A-1030 Vienna Austria
| | - Brigitte Gottsberger
- Department für Botanik und Biodiversitätsforschung; Universität Wien; Rennweg 14 A-1030 Vienna Austria
| | - Jessica L. Ware
- Department of Biology; Rutgers University; 195 University Ave Newark NJ 07102 USA
| |
Collapse
|
31
|
Erwin DH. Early metazoan life: divergence, environment and ecology. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150036. [PMID: 26554036 PMCID: PMC4650120 DOI: 10.1098/rstb.2015.0036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 12/22/2022] Open
Abstract
Recent molecular clock studies date the origin of Metazoa to 750-800 million years ago (Ma), roughly coinciding with evidence from geochemical proxies that oxygen levels rose from less than 0.1% present atmospheric level (PAL) to perhaps 1-3% PAL O2. A younger origin of Metazoa would require greatly increased substitution rates across many clades and many genes; while not impossible, this is less parsimonious. Yet the first fossil evidence for metazoans (the Doushantuo embryos) about 600 Ma is followed by the Ediacaran fossils after 580 Ma, the earliest undisputed bilaterians at 555 Ma, and an increase in the size and morphologic complexity of bilaterians around 542 Ma. This temporal framework suggests a missing 150-200 Myr of early metazoan history that encompasses many apparent novelties in the early evolution of the nervous system. This span includes two major glaciations, and complex marine geochemical changes including major changes in redox and other environmental changes. One possible resolution is that animals of these still unknown Cryogenian and early Ediacaran ecosystems were relatively simple, with highly conserved developmental genes involved in cell-type specification and simple patterning. In this model, complex nervous systems are a convergent phenomenon in bilaterian clades which occurred close to the time that larger metazoans appeared in the fossil record.
Collapse
Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, MRC-121, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| |
Collapse
|
32
|
Gibb GC, Condamine FL, Kuch M, Enk J, Moraes-Barros N, Superina M, Poinar HN, Delsuc F. Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Mol Biol Evol 2015; 33:621-42. [PMID: 26556496 PMCID: PMC4760074 DOI: 10.1093/molbev/msv250] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.
Collapse
Affiliation(s)
- Gillian C Gibb
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden Department of Biological Sciences, University of Alberta, Edmonton, AL, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Nadia Moraes-Barros
- Cibio/Inbio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal Laboratório de Biologia Evolutiva e Conservação de Vertebrados (Labec), Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mariella Superina
- Laboratorio de Endocrinología de la Fauna Silvestre, IMBECU, CCT CONICET Mendoza, Mendoza, Argentina
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| |
Collapse
|
33
|
Pinnow P, Fabrizius A, Pick C, Burmester T. Identification and characterisation of hemocyanin of the fish louse Argulus (Crustacea: Branchiura). J Comp Physiol B 2015; 186:161-8. [PMID: 26515963 DOI: 10.1007/s00360-015-0943-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 02/03/2023]
Abstract
Hemocyanin transports oxygen in the hemolymph of many arthropod species. Within the crustaceans, this copper-containing protein was thought to be restricted to Malacostraca, while other crustacean classes were assumed to employ hemoglobin or lack any respiratory protein. Only recently it has become evident that hemocyanins also occur in Remipedia and Ostracoda. Here we report for the first time the identification and characterisation of hemocyanin in the fish louse Argulus, which belongs to the class of Branchiura. This finding indicates that hemocyanin was the principal oxygen carrier in the stem lineage of the pancrustaceans, but has been lost independently multiple times in crustacean taxa. We obtained the full-length cDNA sequences of two hemocyanin subunits of Argulus foliaceus by a combination of RT-PCR, RACE and Illumina sequencing of the transcriptome. In addition, one full-length and one partial cDNA sequence were derived from the transcriptome data of Argulus siamensis. Western blot analysis confirmed the presence of at least two hemocyanin subunits in A. foliaceus, which are expressed at the mRNA level at a 1:3.5 ratio. The addition to the branchiuran hemocyanin subunits to a multiple sequence alignment of arthropod, hemocyanins improved the phylogenetic resolution within the pancrustacean hemocyanins. Malacostracan, ostracod and branchiuran hemocyanins are distinct from the hexapod and remipede hemocyanins, reinforcing the hypothesis of a close relationship of Remipedia and Hexapoda. Notably, the ostracod hemocyanins are paraphyletic with respect to the branchiuran hemocyanins, indicating ancient divergence and differential loss of distinct subunit types.
Collapse
Affiliation(s)
- Pauline Pinnow
- Institute of Zoology, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Andrej Fabrizius
- Institute of Zoology, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Christian Pick
- Institute of Zoology, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Thorsten Burmester
- Institute of Zoology, University of Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
| |
Collapse
|
34
|
Legendre F, Nel A, Svenson GJ, Robillard T, Pellens R, Grandcolas P. Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence. PLoS One 2015; 10:e0130127. [PMID: 26200914 PMCID: PMC4511787 DOI: 10.1371/journal.pone.0130127] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/18/2015] [Indexed: 12/03/2022] Open
Abstract
Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera-and stem-mantises-would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies.
Collapse
Affiliation(s)
- Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - André Nel
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Gavin J. Svenson
- Department of Invertebrate Zoology, Cleveland Museum of Natural History, Cleveland, Ohio, United States of America
| | - Tony Robillard
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| |
Collapse
|
35
|
Burmester T. Expression and evolution of hexamerins from the tobacco hornworm, Manduca sexta, and other Lepidoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 62:226-34. [PMID: 25497415 DOI: 10.1016/j.ibmb.2014.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/04/2014] [Accepted: 11/28/2014] [Indexed: 05/27/2023]
Abstract
Hexamerins are large hemolymph-proteins that accumulate during the late larval stages of insects. Hexamerins have emerged from hemocyanin, but have lost the ability to bind oxygen. Hexamerins are mainly considered as storage proteins for non-feeding stages, but may also have other functions, e.g. in cuticle formation, transport and immune response. The genome of the hornworm Manduca sexta harbors six hexamerin genes. Two of them code for arylphorins (Msex2.01690, Msex2.15504) and two genes correspond to a methionine-rich hexamerin (Msex2.10735) and a moderately methionine-rich hexamerin (Msex2.01694), respectively. Two other genes do not correspond to any known hexamerin and distantly resemble the arylphorins (Msex2.01691, Msex2.01693). Five of the six hexamerin genes are clustered within ∼45 kb on scaffold 00023, which shows conserved synteny in various lepidopteran genomes. The methionine-rich hexamerin gene is located at a distinct site. M. sexta and other Lepidoptera have lost the riboflavin-binding hexamerin. With the exception of Msex2.01691, which displays low mRNA levels throughout the life cycle, all hexamerins are most highly expressed during pre-wandering phase of the 5th larval instar of M. sexta, supporting their role as storage proteins. Notably, Msex2.01691 is most highly expressed in the brain, suggesting a divergent function. Phylogenetic analyses showed that hexamerin evolution basically follows insect systematics. Lepidoptera display an unparalleled diversity of hexamerins, which exceeds that of other hexapod orders. In contrast to previous analyses, the lepidopteran hexamerins were found monophyletic. Five distinct types of hexamerins have been identified in this order, which differ in terms of amino acid composition and evolutionary history: i. the arylphorins, which are rich in aromatic amino acids (∼20% phenylalanine and tyrosine), ii. the distantly related arylphorin-like hexamerins, iii. the methionine-rich hexamerins, iv. the moderately methionine rich hexamerins, and v. the riboflavin-binding hexamerins.
Collapse
Affiliation(s)
- Thorsten Burmester
- Institute of Zoology and Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany.
| |
Collapse
|
36
|
Burmester T. Evolution of Respiratory Proteins across the Pancrustacea. Integr Comp Biol 2015; 55:792-801. [PMID: 26130703 DOI: 10.1093/icb/icv079] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Respiratory proteins enhance the capacity of the blood for oxygen transport and support intracellular storage and delivery of oxygen. Hemocyanin and hemoglobin are the respiratory proteins that occur in the Pancrustacea. The copper-containing hemocyanins evolved from phenoloxidases in the stem lineage of arthropods. For a long time, hemocyanins had only been known from the malacostracan crustaceans but recent studies identified hemocyanin also in Remipedia, Ostracoda, and Branchiura. Hemoglobins are common in the Branchiopoda but have also been sporadically found in other crustacean classes (Malacostraca, Copepoda, Thecostraca). Respiratory proteins had long been considered unnecessary in the hexapods because of the tracheal system. Only chironomids, some backswimmers, and the horse botfly, which all live under hypoxic conditions, were known exceptions and possess hemoglobins. However, recent data suggest that hemocyanins occur in most ametabolous and hemimetabolous insects. Phylogenetic analysis showed the hemocyanins of insects and Remipedia to be similar, suggesting a close relationship of these taxa. Hemocyanin has been lost in dragonflies, mayflies, and Eumetabola (Hemiptera + Holometabola). In cockroaches and grasshoppers, hemocyanin expression is restricted to the developing embryo while in adults oxygen is supplied solely by the tracheal system. This pattern suggests that hemocyanin was the oxygen-transport protein in the hemolymph of the last common ancestor of the pancrustaceans. The loss was probably associated with miniaturization, a period of restricted availability of oxygen, a change in life-style, or morphological changes. Once lost, hemocyanin was not regained. Some pancrustaceans also possess cellular globin genes with uncertain functions, which are expressed at low levels. When a respiratory protein was again required, hemoglobins evolved several times independently from cellular globins.
Collapse
Affiliation(s)
- Thorsten Burmester
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| |
Collapse
|
37
|
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One 2015; 10:e0130600. [PMID: 26075903 PMCID: PMC4468109 DOI: 10.1371/journal.pone.0130600] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
Background Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor. Method We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade. Results Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development). Conclusions We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.
Collapse
|
38
|
Giribet G. Morphology should not be forgotten in the era of genomics–a phylogenetic perspective. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.01.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Gross V, Mayer G. Neural development in the tardigrade Hypsibius dujardini based on anti-acetylated α-tubulin immunolabeling. EvoDevo 2015; 6:12. [PMID: 26052416 PMCID: PMC4458024 DOI: 10.1186/s13227-015-0008-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/02/2015] [Indexed: 12/15/2022] Open
Abstract
Background The tardigrades (water bears) are a cosmopolitan group of microscopic ecdysozoans found in a variety of aquatic and temporarily wet environments. They are members of the Panarthropoda (Tardigrada + Onychophora + Arthropoda), although their exact position within this group remains contested. Studies of embryonic development in tardigrades have been scarce and have yielded contradictory data. Therefore, we investigated the development of the nervous system in embryos of the tardigrade Hypsibius dujardini using immunohistochemical techniques in conjunction with confocal laser scanning microscopy in an effort to gain insight into the evolution of the nervous system in panarthropods. Results An antiserum against acetylated α-tubulin was used to visualize the axonal processes and general neuroanatomy in whole-mount embryos of the eutardigrade H. dujardini. Our data reveal that the tardigrade nervous system develops in an anterior-to-posterior gradient, beginning with the neural structures of the head. The brain develops as a dorsal, bilaterally symmetric structure and contains a single developing central neuropil. The stomodeal nervous system develops separately and includes at least four separate, ring-like commissures. A circumbuccal nerve ring arises late in development and innervates the circumoral sensory field. The segmental trunk ganglia likewise arise from anterior to posterior and establish links with each other via individual pioneering axons. Each hemiganglion is associated with a number of peripheral nerves, including a pair of leg nerves and a branched, dorsolateral nerve. Conclusions The revealed pattern of brain development supports a single-segmented brain in tardigrades and challenges previous assignments of homology between tardigrade brain lobes and arthropod brain segments. Likewise, the tardigrade circumbuccal nerve ring cannot be homologized with the arthropod ‘circumoral’ nerve ring, suggesting that this structure is unique to tardigrades. Finally, we propose that the segmental ganglia of tardigrades and arthropods are homologous and, based on these data, favor a hypothesis that supports tardigrades as the sister group of arthropods. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0008-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vladimir Gross
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany ; Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| |
Collapse
|
40
|
The nuclear encoded subunits gamma, delta and epsilon from the shrimp mitochondrial F1-ATP synthase, and their transcriptional response during hypoxia. J Bioenerg Biomembr 2015; 47:223-34. [PMID: 25731176 DOI: 10.1007/s10863-015-9605-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/10/2015] [Indexed: 10/23/2022]
Abstract
The mitochondrial FOF1 ATP synthase produces ATP in a reaction coupled to an electrochemical proton gradient generated by the electron transfer chain. The enzyme also hydrolyzes ATP according to the energy requirements of the organism. Shrimp need to overcome low oxygen concentrations in water and other energetic stressors, which in turn lead to mitochondrial responses. The aim of this study was to characterize the full-length cDNA sequences of three subunits that form the central stalk of the F1 catalytic domain of the ATP synthase of the white shrimp Litopenaeus vannamei and their deduced proteins. The effect of hypoxia on shrimp was also evaluated by measuring changes in the mRNA amounts of these subunits. The cDNA sequences of the nucleus-encoded ATPγ, ATPδ and ATPε subunits are 1382, 477 and 277 bp long, respectively. The three deduced amino acid sequences exhibited highly conserved regions when compared to homologous sequences, and specific substitutions found in shrimp subunits are discussed through an homology structural model of F1 ATP-synthase that included the five deduced proteins, which confirm their functional structures and specific characteristics from the cognate complex of ATP synthases. Genes expression was evaluated during hypoxia-reoxygenation, and resulted in a generalized down-regulation of the F1 subunits and no coordinated changes were detected among these five subunits. The reduced mRNA levels suggest a mitochondrial response to an oxidative stress event, similar to that observed at ischemia-reperfusion in mammals. This model analysis and responses to hypoxia-reoxygenation may help to better understand additional mitochondrial adaptive mechanisms.
Collapse
|
41
|
Garwood RJ, Dunlop J. Three-dimensional reconstruction and the phylogeny of extinct chelicerate orders. PeerJ 2014; 2:e641. [PMID: 25405073 PMCID: PMC4232842 DOI: 10.7717/peerj.641] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/08/2014] [Indexed: 12/12/2022] Open
Abstract
Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct arachnid orders. In the Haptopoda, we demonstrate the presence of 'clasp-knife' chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology-in contrast to molecular studies-have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux.
Collapse
Affiliation(s)
- Russell J. Garwood
- School of Earth, Atmospheric and Environmental Sciences and The Manchester X-ray Imaging Facility, School of Materials, The University of Manchester, Manchester, UK
| | - Jason Dunlop
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Berlin, Germany
| |
Collapse
|
42
|
Rainford JL, Hofreiter M, Nicholson DB, Mayhew PJ. Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects. PLoS One 2014; 9:e109085. [PMID: 25275450 PMCID: PMC4183542 DOI: 10.1371/journal.pone.0109085] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/08/2014] [Indexed: 11/18/2022] Open
Abstract
Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward.
Collapse
Affiliation(s)
- James L. Rainford
- Department of Biology, University of York, York, United Kingdom
- * E-mail:
| | - Michael Hofreiter
- Department of Biology, University of York, York, United Kingdom
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - David B. Nicholson
- Department of Biology, University of York, York, United Kingdom
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
| | - Peter J. Mayhew
- Department of Biology, University of York, York, United Kingdom
| |
Collapse
|
43
|
An evolutionary analysis of the Secoviridae family of viruses. PLoS One 2014; 9:e106305. [PMID: 25180860 PMCID: PMC4152289 DOI: 10.1371/journal.pone.0106305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/04/2014] [Indexed: 01/03/2023] Open
Abstract
The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.
Collapse
|
44
|
Andrade SCS, Montenegro H, Strand M, Schwartz ML, Kajihara H, Norenburg JL, Turbeville JM, Sundberg P, Giribet G. A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem. Mol Biol Evol 2014; 31:3206-15. [DOI: 10.1093/molbev/msu253] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
45
|
Mahato S, Morita S, Tucker AE, Liang X, Jackowska M, Friedrich M, Shiga Y, Zelhof AC. Common transcriptional mechanisms for visual photoreceptor cell differentiation among Pancrustaceans. PLoS Genet 2014; 10:e1004484. [PMID: 24991928 PMCID: PMC4084641 DOI: 10.1371/journal.pgen.1004484] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/16/2014] [Indexed: 12/27/2022] Open
Abstract
A hallmark of visual rhabdomeric photoreceptors is the expression of a rhabdomeric opsin and uniquely associated phototransduction molecules, which are incorporated into a specialized expanded apical membrane, the rhabdomere. Given the extensive utilization of rhabdomeric photoreceptors in the eyes of protostomes, here we address whether a common transcriptional mechanism exists for the differentiation of rhabdomeric photoreceptors. In Drosophila, the transcription factors Pph13 and Orthodenticle (Otd) direct both aspects of differentiation: rhabdomeric opsin transcription and rhabdomere morphogenesis. We demonstrate that the orthologs of both proteins are expressed in the visual systems of the distantly related arthropod species Tribolium castaneum and Daphnia magna and that their functional roles are similar in these species. In particular, we establish that the Pph13 homologs have the ability to bind a subset of Rhodopsin core sequence I sites and that these sites are present in key phototransduction genes of both Tribolium and Daphnia. Furthermore, Pph13 and Otd orthologs are capable of executing deeply conserved functions of photoreceptor differentiation as evidenced by the ability to rescue their respective Drosophila mutant phenotypes. Pph13 homologs are equivalent in their ability to direct both rhabdomere morphogenesis and opsin expression within Drosophila, whereas Otd paralogs demonstrate differential abilities to regulate photoreceptor differentiation. Finally, loss-of-function analyses in Tribolium confirm the conserved requirement of Pph13 and Otd in regulating both rhabdomeric opsin transcription and rhabdomere morphogenesis. Taken together, our data identify components of a regulatory framework for rhabdomeric photoreceptor differentiation in Pancrustaceans, providing a foundation for defining ancestral regulatory modules of rhabdomeric photoreceptor differentiation. Visual systems are populated by one of two fundamental types of photoreceptors, ciliary and rhabdomeric. Each photoreceptor type is defined by the opsin molecule expressed and the final morphological form adapted to house the phototransduction machinery. Here we address whether a common transcriptional mechanisms exists for the differentiation of rhabdomeric photoreceptors. We demonstrate that orthologs of two Drosophila (fruit fly) transcription factors, Pph13 and Orthodenticle, are expressed in photoreceptors of Pancrustaceans, Tribolium (red flour beetle) and Daphnia (water flea), and are capable of executing conserved functions of rhabdomeric photoreceptor differentiation. In particular, Tribolium and Daphnia orthologs are capable of substituting and rescuing the photoreceptor differentiation defects observed in their corresponding Drosophila mutants. Furthermore, loss of function analysis in Tribolium of both Pph13 and orthodenticle genes demonstrate they regulate opsin transcription and morphogenesis of the photoreceptor apical membrane. Our data illuminate a framework for rhabdomeric photoreceptor differentiation and provide the foundation for defining the ancestral regulatory modules for rhabdomeric differentiation and potential modifications that underlie the functional diversity observed in rhabdomeric photoreceptors.
Collapse
Affiliation(s)
- Simpla Mahato
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Shinichi Morita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Abraham E. Tucker
- Department of Biology, Southern Arkansas University, Magnolia, Arkansas, United States of America
| | - Xulong Liang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Magdalena Jackowska
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Yasuhiro Shiga
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Andrew C. Zelhof
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| |
Collapse
|
46
|
Rehm P, Meusemann K, Borner J, Misof B, Burmester T. Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing. Mol Phylogenet Evol 2014; 77:25-33. [PMID: 24732681 DOI: 10.1016/j.ympev.2014.04.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 02/02/2023]
Abstract
Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.
Collapse
Affiliation(s)
- Peter Rehm
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany; CSIRO Ecosystem Sciences, Australian National Insect Collection, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Janus Borner
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany
| | - Thorsten Burmester
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany.
| |
Collapse
|
47
|
Evolution of PAS domains and PAS-containing genes in eukaryotes. Chromosoma 2014; 123:385-405. [PMID: 24699836 DOI: 10.1007/s00412-014-0457-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/21/2014] [Accepted: 03/11/2014] [Indexed: 01/18/2023]
Abstract
The PAS domains are signal modules, which are widely distributed in proteins across all kingdoms of life. They are common in photoreceptors and transcriptional regulators of eukaryotic circadian clocks q(bHLH-PAS proteins and PER in animals; PHY and ZTL in plants; and WC-1, 2, and VVD in fungi) and possess mainly protein-protein interaction and light-sensing functions. We conducted several evolutionary analyses of the PAS superfamily. Although the whole superfamily evolved primarily under strong purifying selection (average ω ranges from 0.0030 to 0.1164), some lineages apparently experienced strong episodic positive selection at some periods of the evolution. Although the PAS domains from different proteins vary in sequence and length, but they maintain a fairly conserved 3D structure, which is determined by only eight residues. The WC-1 and WC- 2, bHLH-PAS, and P er genes probably originated in the Neoproterozoic Era (1000-542 Mya), plant P hy and ZTL evolved in the Paleozoic (541-252 Mya), which might be a result of adaptation to the major climate and global light regime changes having occurred in those eras.
Collapse
|
48
|
Fernández R, Laumer CE, Vahtera V, Libro S, Kaluziak S, Sharma PP, Pérez-Porro AR, Edgecombe GD, Giribet G. Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Mol Biol Evol 2014; 31:1500-13. [PMID: 24674821 DOI: 10.1093/molbev/msu108] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.
Collapse
Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Christopher E Laumer
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Varpu Vahtera
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MAZoological Museum, Department of Biology, University of Turku, Turku, Finland
| | - Silvia Libro
- Marine Science Center, Northeastern University, Nahant, MA
| | | | - Prashant P Sharma
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alicia R Pérez-Porro
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MACentre d'Estudis Avançats de Blanes (CEAB-CSIC), Catalonia, Spain
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| |
Collapse
|
49
|
Pick C, Scherbaum S, Hegedüs E, Meyer A, Saur M, Neumann R, Markl J, Burmester T. Structure, diversity and evolution of myriapod hemocyanins. FEBS J 2014; 281:1818-33. [DOI: 10.1111/febs.12742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/23/2014] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Pick
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Samantha Scherbaum
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Elöd Hegedüs
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Andreas Meyer
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Michael Saur
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Ruben Neumann
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Jürgen Markl
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| |
Collapse
|
50
|
Brewer MS, Bond JE. Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses. PLoS One 2013; 8:e79935. [PMID: 24236165 PMCID: PMC3827447 DOI: 10.1371/journal.pone.0079935] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 10/02/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The ancient and diverse, yet understudied arthropod class Diplopoda, the millipedes, has a muddled taxonomic history. Despite having a cosmopolitan distribution and a number of unique and interesting characteristics, the group has received relatively little attention; interest in millipede systematics is low compared to taxa of comparable diversity. The existing classification of the group comprises 16 orders. Past attempts to reconstruct millipede phylogenies have suffered from a paucity of characters and included too few taxa to confidently resolve relationships and make formal nomenclatural changes. Herein, we reconstruct an ordinal-level phylogeny for the class Diplopoda using the largest character set ever assembled for the group. METHODS Transcriptomic sequences were obtained from exemplar taxa representing much of the diversity of millipede orders using second-generation (i.e., next-generation or high-throughput) sequencing. These data were subject to rigorous orthology selection and phylogenetic dataset optimization and then used to reconstruct phylogenies employing Bayesian inference and maximum likelihood optimality criteria. Ancestral reconstructions of sperm transfer appendage development (gonopods), presence of lateral defense secretion pores (ozopores), and presence of spinnerets were considered. The timings of major millipede lineage divergence points were estimated. RESULTS The resulting phylogeny differed from the existing classifications in a number of fundamental ways. Our phylogeny includes a grouping that has never been described (Juliformia+Merocheta+Stemmiulida), and the ancestral reconstructions suggest caution with respect to using spinnerets as a unifying characteristic for the Nematophora. Our results are shown to have significantly stronger support than previous hypotheses given our data. Our efforts represent the first step toward obtaining a well-supported and robust phylogeny of the Diplopoda that can be used to answer many questions concerning the evolution of this ancient and diverse animal group.
Collapse
Affiliation(s)
- Michael S. Brewer
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, United States of America
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - Jason E. Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| |
Collapse
|