1
|
Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
Collapse
Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
| |
Collapse
|
2
|
Dotan E, Alburquerque M, Wygoda E, Huchon D, Pupko T. GenomeFLTR: filtering reads made easy. Nucleic Acids Res 2023:7161531. [PMID: 37177997 DOI: 10.1093/nar/gkad410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
In the last decade, advances in sequencing technology have led to an exponential increase in genomic data. These new data have dramatically changed our understanding of the evolution and function of genes and genomes. Despite improvements in sequencing technologies, identifying contaminated reads remains a complex task for many research groups. Here, we introduce GenomeFLTR, a new web server to filter contaminated reads. Reads are compared against existing sequence databases from various representative organisms to detect potential contaminants. The main features implemented in GenomeFLTR are: (i) automated updating of the relevant databases; (ii) fast comparison of each read against the database; (iii) the ability to create user-specified databases; (iv) a user-friendly interactive dashboard to investigate the origin and frequency of the contaminations; (v) the generation of a contamination-free file. Availability: https://genomefltr.tau.ac.il/.
Collapse
Affiliation(s)
- Edo Dotan
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Alburquerque
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Elya Wygoda
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
3
|
Gupta A, Haddas-Sasson M, Gayer K, Huchon D. Author Correction: Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee. Sci Rep 2023; 13:4565. [PMID: 36941298 PMCID: PMC10027886 DOI: 10.1038/s41598-023-31318-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Affiliation(s)
- Aditya Gupta
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel.
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel.
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Kfir Gayer
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel.
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel.
| |
Collapse
|
4
|
Liberman R, Benayahu Y, Huchon D. Octocorals in the Gulf of Aqaba exhibit high photosymbiont fidelity. Front Microbiol 2022; 13:1005471. [PMID: 36504779 PMCID: PMC9732034 DOI: 10.3389/fmicb.2022.1005471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/25/2022] [Indexed: 11/26/2022] Open
Abstract
Symbiotic associations, widespread in terrestrial and marine ecosystems, are of considerable ecological importance. Many tropical coral species are holobionts, formed by the obligate association between a cnidarian host and endosymbiotic dinoflagellates of the family Symbiodiniaceae. The latter are abundant on coral reefs from very shallow water down to the upper mesophotic zone (30-70 m). The research on scleractinians has revealed that the photosymbiont lineages present in the cnidarian host play an important role in the coral's ability to thrive under different environmental conditions, such as light regime and temperature. However, little is known regarding octocoral photosymbionts, and in particular regarding those found deeper than 30 m. Here, we used ribosomal (ITS2) and chloroplast (23S) markers to uncover, for the first time, the dominant Symbiodiniaceae taxa present in 19 mesophotic octocoral species (30-70 m depth) from the Gulf of Aqaba/Eilat (northern Red Sea). In addition, using high-throughput sequencing of the ITS2 region we characterized both the dominant and the rare Symbiodiniaceae lineages found in several species across depth. The phylogenetic analyses of both markers were in agreement and revealed that most of the studied mesophotic octocorals host the genus Cladocopium. Litophyton spp. and Klyxum utinomii were exceptions, as they harbored Symbiodinium and Durusdinium photosymbionts, respectively. While the dominant algal lineage of each coral species did not vary across depth, the endosymbiont community structure significantly differed between host species, as well as between different depths for some host species. The findings from this study contribute to the growing global-catalogue of Cnidaria-Symbiodiniaceae associations. Unravelling the Symbiodiniaceae composition in octocoral holobionts across environmental gradients, depth in particular, may enable a better understanding of how specialized those associations are, and to what extent coral holobionts are able to modify their photosymbionts.
Collapse
Affiliation(s)
- Ronen Liberman
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel,The Interuniversity Institute for Marine Sciences, Eilat, Israel,*Correspondence: Ronen Liberman,
| | - Yehuda Benayahu
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Dorothée Huchon
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
5
|
Novosolov M, Yahalomi D, Chang ES, Fiala I, Cartwright P, Huchon D. The Phylogenetic Position of the Enigmatic, Polypodium hydriforme (Cnidaria, Polypodiozoa): Insights from Mitochondrial Genomes. Genome Biol Evol 2022; 14:6648524. [PMID: 35867352 PMCID: PMC9380995 DOI: 10.1093/gbe/evac112] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Polypodium hydriforme is an enigmatic parasite that belongs to the phylum Cnidaria. Its taxonomic position has been debated: whereas it was previously suggested to be part of Medusozoa, recent phylogenomic analyses based on nuclear genes support the view that P. hydriforme and Myxozoa form a clade called Endocnidozoa. Medusozoans have linear mitochondrial (mt) chromosomes, whereas myxozoans, as most metazoan species, have circular chromosomes. In this work, we determined the structure of the mt genome of P. hydriforme, using Illumina and Oxford Nanopore Technologies reads, and showed that it is circular. This suggests that P. hydriforme is not nested within Medusozoa, as this would entail linearization followed by recirculation. Instead, our results support the view that P. hydriforme is a sister clade to Myxozoa, and mt linearization in the lineage leading to medusozoans occurred after the divergence of Myxozoa + P. hydriforme. Detailed analyses of the assembled P. hydriforme mt genome show that: (1) it is encoded on a single circular chromosome with an estimated size of ∼93,000 base pairs, making it one of the largest metazoan mt genomes; (2) around 78% of the genome encompasses a noncoding region composed of several repeat types; (3) similar to Myxozoa, no mt tRNAs were identified; (4) the codon TGA is a stop codon and does not encode for tryptophan as in other cnidarians; (5) similar to myxozoan mt genomes, it is extremely fast evolving.
Collapse
Affiliation(s)
- Maria Novosolov
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - E Sally Chang
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Haworth Hall, Lawrence, KS, 66045, USA.,Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Fiala
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Branišovská 31, 370 05 České Budĕjovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budĕjovice, Czech Republic
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Haworth Hall, Lawrence, KS, 66045, USA
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
6
|
Gupta A, Haddas-Sasson M, Gayer K, Huchon D. Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee. Sci Rep 2022; 12:10049. [PMID: 35710685 PMCID: PMC9203526 DOI: 10.1038/s41598-022-13215-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/23/2022] [Indexed: 11/09/2022] Open
Abstract
Mullets (Mugilidae) are economically important fish in Israel. Two species of mugilids (i.e., the thinlip mullet Chelon ramada and the flathead grey mullet Mugil cephalus) have been stocked in the Sea of Galilee (Lake Kinneret) in order to increase fishermen's income and lake water quality. These catadromous species do not reproduce in the lake, consequently, fingerlings have been introduced every year since 1958. Following a survey of myxozoan infections in the Sea of Galilee, we described Myxobolus pupkoi n. sp. infecting the gill arches, and reported Myxobolus exiguus from visceral peritoneum and gall bladder of C. ramada. The prevalence of infection of both Myxobolus pupkoi n. sp. and M. exiguus were 11.5% (2/23). Our study indicates that the parasites infecting C. ramada belong to a lineage of myxozoans infecting mugilids. This result suggests that the infection took place in the Mediterranean Sea, where the fingerlings were caught, before their introduction into the Sea of Galilee. Since 2018 only farm-raised fingerlings have been introduced. We thus recommend to closely monitor the presence of these parasites in the future to determine if the presence of parasites disappear with the introduction of farm-raised fingerlings.
Collapse
Affiliation(s)
- Aditya Gupta
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel.
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel.
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Kfir Gayer
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel-Aviv, Israel.
- Steinhardt Natural History Museum, Tel Aviv University, 6997801, Tel-Aviv, Israel.
| |
Collapse
|
7
|
Alama-Bermejo G, Hernández-Orts JS, Huchon D, Atkinson SD. Two novel myxosporean parasite species of Ceratomyxa Thélohan, 1892 from the banded cusk-eel Raneya brasiliensis (Kaup) (Ophidiiformes: Ophidiidae) off Patagonia, Argentina. Parasitol Int 2021; 85:102433. [PMID: 34371156 DOI: 10.1016/j.parint.2021.102433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
We described two novel myxozoan parasite species Ceratomyxa argentina n. sp. and Ceratomyxa raneyae n. sp. from the gall bladder of Raneya brasiliensis (Kaup) from the Patagonian coast of Argentina. Both species can be distinguished from other ceratomyxids by myxospore and polar capsule (nematocyst) morphology and morphometry, fish host and geographic locality. Phylogenetic reconstruction using ssrDNA gene sequences showed that the two new species are placed in a long-branching ceratomyxid clade which also include Ceratomyxa appendiculata Thélohan, 1892, Ceratomyxa anko Freeman, Yokoyama and Ogawa, 2008, Ceratomyxa pantherini Gunter, Burger and Adlard, 2010 and Pseudoalataspora kovalevae Kalavati, MacKenzie, Collins, Hemmingsen and Brickle, 2013. This study documents additional biodiversity of marine myxozoans in the South Atlantic, a region still largely unexplored for this group of parasitic cnidarians.
Collapse
Affiliation(s)
- Gema Alama-Bermejo
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37 005 České Budějovice, Czech Republic; Department of Microbiology, Oregon State University, 97331 Corvallis, Oregon, USA.
| | - Jesús S Hernández-Orts
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37 005 České Budějovice, Czech Republic
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel; The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331 Corvallis, Oregon, USA
| |
Collapse
|
8
|
Kyger R, Luzuriaga-Neira A, Layman T, Milkewitz Sandberg TO, Singh D, Huchon D, Peri S, Atkinson SD, Bartholomew JL, Yi SV, Alvarez-Ponce D. Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation. Mol Biol Evol 2021; 38:393-404. [PMID: 32898240 PMCID: PMC7826176 DOI: 10.1093/molbev/msaa214] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.
Collapse
Affiliation(s)
- Ryan Kyger
- Department of Biology, University of Nevada, Reno, NV
| | | | - Thomas Layman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | | | - Devika Singh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Dorothée Huchon
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Sateesh Peri
- Department of Biology, University of Nevada, Reno, NV
| | | | | | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | | |
Collapse
|
9
|
Gordon T, Upadhyay AK, Manni L, Huchon D, Shenkar N. And Then There Were Three…: Extreme Regeneration Ability of the Solitary Chordate Polycarpa mytiligera. Front Cell Dev Biol 2021; 9:652466. [PMID: 33937252 PMCID: PMC8083962 DOI: 10.3389/fcell.2021.652466] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Extensive regenerative ability is a common trait of animals capable of asexual development. The current study reveals the extraordinary regeneration abilities of the solitary ascidian Polycarpa mytiligera. Dissection of a single individual into separate fragments along two body axes resulted in the complete regeneration of each fragment into an independent, functional individual. The ability of a solitary ascidian, incapable of asexual development, to achieve bidirectional regeneration and fully regenerate all body structures and organs is described here for the first time. Amputation initiated cell proliferation in proximity to the amputation line. Phylogenetic analysis demonstrated the close affinity of P. mytiligera to colonial species. This evolutionary proximity suggests the ability for regeneration as an exaptation feature for colonial lifestyle. P. mytiligera’s exceptional regenerative abilities and phylogenetic position highlight its potential to serve as a new comparative system for studies seeking to uncover the evolution of regeneration and coloniality among the chordates.
Collapse
Affiliation(s)
- Tal Gordon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Arnav Kumar Upadhyay
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
10
|
Shpirer E, Haddas-Sasson M, Spivak-Glater M, Feldstein T, Meiri S, Huchon D. Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences. MAMMALIA 2020. [DOI: 10.1515/mammalia-2019-0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The number of shrew species in Israel has been and still is the subject of debate. In this work we used for the first time a molecular marker, the cytochrome b gene, to investigate the number and identity of shrew species in Israel. Our molecular results confirmed the presence of four species: Crocidura leucodon, Crocidura suaveolens gueldenstaedtii, Crocidura ramona, and Suncus etruscus. The C. ramona sequences were found to differ from all other Crocidura species sequenced to date, supporting its status as a distinct species. Whether it is conspecific with Crocidura portali (described in 1920 from Israel and usually synonymized with C. suaveolens), will require additional study. The sequences of Israeli C. suaveolens were found to be very similar to those of Iran, Turkey, and Georgia (i.e., C. suaveolens gueldenstaedtii), in agreement with previous studies. The Israeli C. leucodon sequences, however, formed a distinct clade among C. leucodon. Finally, the S. etruscus sequences clustered with sequences from France, Italy, and Iran.
Collapse
Affiliation(s)
- Erez Shpirer
- School of Zoology , Tel Aviv University , Ramat Aviv , 69978, Tel Aviv , Israel
| | | | - Maya Spivak-Glater
- School of Zoology , Tel Aviv University , Ramat Aviv , 69978, Tel Aviv , Israel
| | - Tamar Feldstein
- School of Zoology , Tel Aviv University , Ramat Aviv , 69978, Tel Aviv , Israel
- The Steinhardt Museum of Natural History and National Research Center , Tel-Aviv University , Tel Aviv , Israel
| | - Shai Meiri
- School of Zoology , Tel Aviv University , Ramat Aviv , 69978, Tel Aviv , Israel
- The Steinhardt Museum of Natural History and National Research Center , Tel-Aviv University , Tel Aviv , Israel
| | - Dorothée Huchon
- School of Zoology , Tel Aviv University , Ramat Aviv , 69978, Tel Aviv , Israel
- The Steinhardt Museum of Natural History and National Research Center , Tel-Aviv University , Tel Aviv , Israel
| |
Collapse
|
11
|
Anava S, Neuhof M, Gingold H, Sagy O, Munters A, Svensson EM, Afshinnekoo E, Danko D, Foox J, Shor P, Riestra B, Huchon D, Mason CE, Mizrahi N, Jakobsson M, Rechavi O. Illuminating Genetic Mysteries of the Dead Sea Scrolls. Cell 2020; 181:1218-1231.e27. [PMID: 32492404 DOI: 10.1016/j.cell.2020.04.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/01/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022]
Abstract
The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.
Collapse
Affiliation(s)
- Sarit Anava
- Department of Neurobiology, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Moran Neuhof
- Department of Neurobiology, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Or Sagy
- Department of Neurobiology, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Arielle Munters
- Human Evolution, Department of Organismal Biology and SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology and SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitate Prediction, New York, NY 10065, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitate Prediction, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitate Prediction, New York, NY 10065, USA
| | - Pnina Shor
- Dead Sea Scroll Projects, Israel Antiquities Authority, Jerusalem 91710, Israel
| | - Beatriz Riestra
- Dead Sea Scroll Projects, Israel Antiquities Authority, Jerusalem 91710, Israel
| | - Dorothée Huchon
- Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv 6997801, Israel; Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitate Prediction, New York, NY 10065, USA
| | - Noam Mizrahi
- Department of Biblical Studies, The Lester and Sally Entin Faculty of Humanities, Tel Aviv University, Tel-Aviv 6997801, Israel.
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden.
| | - Oded Rechavi
- Department of Neurobiology, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel.
| |
Collapse
|
12
|
Fromm A, Atkinson SD, Alama-Bermejo G, Cartwright P, Bartholomew JL, Huchon D. A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes). Mitochondrial DNA B Resour 2018; 4:1-4. [PMID: 33365395 PMCID: PMC7510595 DOI: 10.1080/23802359.2018.1532824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6 – D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae.
Collapse
Affiliation(s)
- Amir Fromm
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Gema Alama-Bermejo
- Center for Applied Research and Technology Transference in Marine Resources Almirante Storni (CIMAS-CCT CONICET-CENPAT), San Antonio Oeste, Argentina
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
13
|
Shpirer E, Diamant A, Cartwright P, Huchon D. A genome wide survey reveals multiple nematocyst-specific genes in Myxozoa. BMC Evol Biol 2018; 18:138. [PMID: 30208843 PMCID: PMC6134521 DOI: 10.1186/s12862-018-1253-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/22/2018] [Indexed: 12/02/2022] Open
Abstract
Background Myxozoa represents a diverse group of microscopic endoparasites whose life cycle involves two hosts: a vertebrate (usually a fish) and an invertebrate (usually an annelid worm). Despite lacking nearly all distinguishing animal characteristics, given that each life cycle stage consists of no more than a few cells, molecular phylogenetic studies have revealed that myxozoans belong to the phylum Cnidaria, which includes corals, sea anemones, and jellyfish. Myxozoa, however, do possess a polar capsule; an organelle that is homologous to the stinging structure unique to Cnidaria: the nematocyst. Previous studies have identified in Myxozoa a number of protein-coding genes that are specific to nematocytes (the cells producing nematocysts) and thus restricted to Cnidaria. Determining which other genes are also homologous with the myxozoan polar capsule genes could provide insight into both the conservation and changes that occurred during nematocyst evolution in the transition to endoparasitism. Results Previous studies have examined the phylogeny of two cnidarian-restricted gene families: minicollagens and nematogalectins. Here we identify and characterize seven additional cnidarian-restricted genes in myxozoan genomes using a phylogenetic approach. Four of the seven had never previously been identified as cnidarian-specific and none have been studied in a phylogenetic context. A majority of the proteins appear to be involved in the structure of the nematocyst capsule and tubule. No venom proteins were identified among the cnidarian-restricted genes shared by myxozoans. Conclusions Given the highly divergent forms that comprise Cnidaria, obtaining insight into the processes underlying their ancient diversification remains challenging. In their evolutionary transition to microscopic endoparasites, myxozoans lost nearly all traces of their cnidarian ancestry, with the one prominent exception being their nematocysts (or polar capsules). Thus nematocysts, and the genes that code for their structure, serve as rich sources of information to support the cnidarian origin of Myxozoa. Electronic supplementary material The online version of this article (10.1186/s12862-018-1253-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erez Shpirer
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA.
| | - Dorothée Huchon
- School of Zoology, Tel Aviv University, Tel Aviv, Israel. .,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
14
|
Arafat H, Alamaru A, Gissi C, Huchon D. Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida. BMC Evol Biol 2018; 18:65. [PMID: 29703131 PMCID: PMC5924465 DOI: 10.1186/s12862-018-1186-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150-200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis. RESULTS The mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species. CONCLUSIONS Since Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum.
Collapse
Affiliation(s)
- Hanan Arafat
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel
| | - Ada Alamaru
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy.,IBIOM, Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, CNR (Italy), Bari, Italy
| | - Dorothée Huchon
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel. .,The Steinhardt Museum of Natural History and National Research Center, Tel-Aviv University, Tel-Aviv, Israel.
| |
Collapse
|
15
|
Ostersetzer-Biran O, Lane N, Pomiankowski A, Burton R, Arnqvist G, Filipovska A, Huchon D, Mishmar D. The First Mitochondrial Genomics and Evolution SMBE-Satellite Meeting: A New Scientific Symbiosis. Genome Biol Evol 2017; 9:3054-3058. [PMID: 29106528 PMCID: PMC5714122 DOI: 10.1093/gbe/evx227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 11/12/2022] Open
Abstract
The central role of the mitochondrion for cellular and organismal metabolism is well known, yet its functional role in evolution has rarely been featured in leading international conferences. Moreover, the contribution of mitochondrial genetics to complex disease phenotypes is particularly important, and although major advances have been made in the field of genomics, mitochondrial genomic data have in many cases been overlooked. Accumulating data and new knowledge support a major contribution of this maternally inherited genome, and its interactions with the nucleus, to both major evolutionary processes and diverse disease phenotypes. These advances encouraged us to assemble the first Mitochondrial Genomics and Evolution (MGE) meeting-an SMBE satellite and Israeli Science foundation international conference (Israel, September 2017). Here, we report the content and outcome of the MGE meeting (https://www.mge2017.com/; last accessed November 5, 2017).
Collapse
Affiliation(s)
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Ron Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego
| | - Göran Arnqvist
- Department of Ecology and Genetics, University of Uppsala, Sweden
| | - Aleksandra Filipovska
- School of Molecular Sciences and The Harry Perkins Institute of Medical Research, The University of Western Australia, Australia
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
16
|
Yahalomi D, Haddas-Sasson M, Rubinstein ND, Feldstein T, Diamant A, Huchon D. The Multipartite Mitochondrial Genome of Enteromyxum leei (Myxozoa): Eight Fast-Evolving Megacircles. Mol Biol Evol 2017; 34:1551-1556. [PMID: 28333349 DOI: 10.1093/molbev/msx072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochondrial (mt) genome of Enteromyxum leei and reevaluate the mt genome structure of Kudoa iwatai. Although the typical animal mt genome is a compact, 13-25 kb, circular chromosome, the mt genome of E. leei was found to be fragmented into eight circular chromosomes of ∼23 kb, making it the largest described animal mt genome. Each chromosome was found to harbor a large noncoding region (∼15 kb), nearly identical between chromosomes. The protein coding genes show an unusually high rate of sequence evolution and possess little similarity to their cnidarian homologs. Only five protein coding genes could be identified and no tRNA genes. Surprisingly, the mt genome of K. iwatai was also found to be composed of two chromosomes. These observations confirm the remarkable plasticity of myxozoan mt genomes.
Collapse
Affiliation(s)
- Dayana Yahalomi
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nimrod D Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, Israel
| | - Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
17
|
Meiri M, Stockhammer PW, Marom N, Bar-Oz G, Sapir-Hen L, Morgenstern P, Macheridis S, Rosen B, Huchon D, Maran J, Finkelstein I. Eastern Mediterranean Mobility in the Bronze and Early Iron Ages: Inferences from Ancient DNA of Pigs and Cattle. Sci Rep 2017; 7:701. [PMID: 28386123 PMCID: PMC5429671 DOI: 10.1038/s41598-017-00701-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/08/2017] [Indexed: 11/14/2022] Open
Abstract
The Late Bronze of the Eastern Mediterranean (1550–1150 BCE) was a period of strong commercial relations and great prosperity, which ended in collapse and migration of groups to the Levant. Here we aim at studying the translocation of cattle and pigs during this period. We sequenced the first ancient mitochondrial and Y chromosome DNA of cattle from Greece and Israel and compared the results with morphometric analysis of the metacarpal in cattle. We also increased previous ancient pig DNA datasets from Israel and extracted the first mitochondrial DNA for samples from Greece. We found that pigs underwent a complex translocation history, with links between Anatolia with southeastern Europe in the Bronze Age, and movement from southeastern Europe to the Levant in the Iron I (ca. 1150–950 BCE). Our genetic data did not indicate movement of cattle between the Aegean region and the southern Levant. We detected the earliest evidence for crossbreeding between taurine and zebu cattle in the Iron IIA (ca. 900 BCE). In light of archaeological and historical evidence on Egyptian imperial domination in the region in the Late Bronze Age, we suggest that Egypt attempted to expand dry farming in the region in a period of severe droughts.
Collapse
Affiliation(s)
- Meirav Meiri
- Institute of Archaeology, Tel Aviv University, Tel Aviv, 69978, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Schellingstraße 12, 80799, München, Germany
| | - Nimrod Marom
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Lidar Sapir-Hen
- Institute of Archaeology, Tel Aviv University, Tel Aviv, 69978, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peggy Morgenstern
- Institute for Prehistory, Protohistory and Near Eastern Archaeology, University of Heidelberg, Marstallhof 4, 69117, Heidelberg, Germany
| | - Stella Macheridis
- Department of Archaeology and Ancient History, Lund University, Helgonvägen 3, 223 63, Lund, Sweden
| | - Baruch Rosen
- Israel Antiquities Authority, POB 180, Atlit, 30300, Israel
| | - Dorothée Huchon
- Department of Zoology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Joseph Maran
- Institute for Prehistory, Protohistory and Near Eastern Archaeology, University of Heidelberg, Marstallhof 4, 69117, Heidelberg, Germany
| | | |
Collapse
|
18
|
Shenkar N, Koplovitz G, Dray L, Gissi C, Huchon D. Back to solitude: Solving the phylogenetic position of the Diazonidae using molecular and developmental characters. Mol Phylogenet Evol 2016; 100:51-56. [DOI: 10.1016/j.ympev.2016.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/27/2016] [Accepted: 04/01/2016] [Indexed: 01/13/2023]
|
19
|
Huchon D, Szitenberg A, Shefer S, Ilan M, Feldstein T. Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida. BMC Evol Biol 2015; 15:278. [PMID: 26653218 PMCID: PMC4676843 DOI: 10.1186/s12862-015-0556-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 12/03/2015] [Indexed: 11/21/2022] Open
Abstract
Background Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges. Results We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinellapverrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals’ mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns. Conclusions The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0556-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Amir Szitenberg
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,Current address: School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK.
| | - Sigal Shefer
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
| |
Collapse
|
20
|
Abstract
It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships among various taxonomical groups. However, indels are never directly observed but rather inferred from the alignment and thus indel-based inference may be sensitive to alignment errors. It is hypothesized that phylogenetic reconstruction would be more accurate if it relied only on a subset of reliable indels instead of the entire indel data. Here, we developed a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments. Our approach is based on the assumption that indels that are consistently present in most alternative alignments are more reliable compared with indels that appear only in a small subset of these alignments. Using simulated and empirical data, we studied the impact of filtering and weighting indels by their reliability scores on the accuracy of indel-based phylogenetic reconstruction. The new method is available as a web-server at http://guidance.tau.ac.il/RELINDEL/.
Collapse
Affiliation(s)
- Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Ofir Cohen
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel Present address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| |
Collapse
|
21
|
Shpirer E, Chang ES, Diamant A, Rubinstein N, Cartwright P, Huchon D. Diversity and evolution of myxozoan minicollagens and nematogalectins. BMC Evol Biol 2014; 14:205. [PMID: 25262812 PMCID: PMC4195985 DOI: 10.1186/s12862-014-0205-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background Myxozoa are a diverse group of metazoan parasites with a very simple organization, which has for decades eluded their evolutionary origin. Their most prominent and characteristic feature is the polar capsule: a complex intracellular structure of the myxozoan spore, which plays a role in host infection. Striking morphological similarities have been found between myxozoan polar capsules and nematocysts, the stinging structures of cnidarians (corals, sea anemones and jellyfish) leading to the suggestion that Myxozoa and Cnidaria share a more recent common ancestry. This hypothesis has recently been supported by phylogenomic evidence and by the identification of a nematocyst specific minicollagen gene in the myxozoan Tetracapsuloides bryosalmonae. Here we searched genomes and transcriptomes of several myxozoan taxa for the presence of additional cnidarian specific genes and characterized these genes within a phylogenetic context. Results Illumina assemblies of transcriptome or genome data of three myxozoan species (Enteromyxum leei, Kudoa iwatai, and Sphaeromyxa zaharoni) and of the enigmatic cnidarian parasite Polypodium hydriforme (Polypodiozoa) were mined using tBlastn searches with nematocyst-specific proteins as queries. Several orthologs of nematogalectins and minicollagens were identified. Our phylogenetic analyses indicate that myxozoans possess three distinct minicollagens. We found that the cnidarian repertoire of nematogalectins is more complex than previously thought and we identified additional members of the nematogalectin family. Cnidarians were found to possess four nematogalectin/ nematogalectin-related genes, while in myxozoans only three genes could be identified. Conclusions Our results demonstrate that myxozoans possess a diverse array of genes that are taxonomically restricted to Cnidaria. Characterization of these genes provide compelling evidence that polar capsules and nematocysts are homologous structures and that myxozoans are highly degenerate cnidarians. The diversity of minicollagens was higher than previously thought, with the presence of three minicollagen genes in myxozoans. Our phylogenetic results suggest that the different myxozoan sequences are the results of ancient divergences within Cnidaria and not of recent specializations of the polar capsule. For both minicollagen and nematogalectin, our results show that myxozoans possess less gene copies than their cnidarian counter parts, suggesting that the polar capsule gene repertoire was simplified with their reduced body plan. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0205-0) contains supplementary material, which is available to authorized users.
Collapse
|
22
|
Dray L, Neuhof M, Diamant A, Huchon D. The complete mitochondrial genome of the devil firefish Pterois miles (Bennett, 1828) (Scorpaenidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:783-4. [PMID: 25103446 DOI: 10.3109/19401736.2014.945565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the devil firefish Pterois miles (Bennett, 1828) was obtained using next generation sequencing approaches. The genome sequence was comprised of 16,497 bp exhibiting the standard vertebrate mitochondrial gene arrangement. Regions of gene overlap, tRNA lengths, as well as start and stop codons were similar to those observed in closely related families (i.e. Sebastidae, Peristediidae). Phylogenetic reconstructions support the polyphyly of Scorpaeniformes, and confirm the close relationship of Scorpaenidae and Sebastidae.
Collapse
Affiliation(s)
- Liran Dray
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Moran Neuhof
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Arik Diamant
- b National Center for Mariculture, Israel Oceanographic and Limnological Research , Eilat , Israel
| | - Dorothée Huchon
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| |
Collapse
|
23
|
Dray L, Neuhof M, Diamant A, Huchon D. The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:781-2. [PMID: 24963773 DOI: 10.3109/19401736.2014.928861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.
Collapse
Affiliation(s)
- Liran Dray
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Moran Neuhof
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| | - Arik Diamant
- b National Center for Mariculture, Israel Oceanographic and Limnological Research , Eilat Israel
| | - Dorothée Huchon
- a Department of Zoology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel and
| |
Collapse
|
24
|
Diamant A, Rothman SBS, Goren M, Galil BS, Yokes MB, Szitenberg A, Huchon D. Biology of a new xenoma-forming gonadotropic microsporidium in the invasive blotchfin dragonet Callionymus filamentosus. Dis Aquat Organ 2014; 109:35-54. [PMID: 24781795 DOI: 10.3354/dao02718] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A gonadotropic microsporidian parasite, Obruspora papernae gen. et sp. nov. (Microsporidia: Enterocytozoonidae), is described from Callionymus filamentosus (Teleostei: Callionymidae) in the Mediterranean Sea. The host, a Red Sea invasive species which entered the Mediterranean through the Suez Canal, was first collected in the Levant Basin in 1953, whereas its parasite went unobserved until 2008. Analysis of partial small subunit ribosomal gene sequences (SSU rDNA) placed the new species within the Nucleospora, Desmozoon, and Paranucleospora clade, and as it differs from each of them, it is assigned to a new genus. The development of the parasite is described, and the biological mechanisms underlying this parasite-host system are analyzed. Prevalence of infection approached 80% in female samples throughout most of the year. Males showed no signs of infection, but parasite rDNA was detected in male internal organs. The parasite-induced xenomas progressively occupied and eventually replaced much of the ovary, in some cases producing effective castration. Despite high levels of parasite infection, current trawl fishery statistics indicate that the abundance of Mediterranean populations of the host remains high. The parasite impact on the host population dynamics is unclear. Possible effects of the new microsporidian parasite on the reproductive effort of C. filamentosus and the potential role of another parasite, the ectoparasitic copepod Lernanthropus callionymicola, as an additional host in the life cycle of O. papernae, require further investigation.
Collapse
Affiliation(s)
- Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, PO Box 1212, Eilat 88112, Israel
| | | | | | | | | | | | | |
Collapse
|
25
|
Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, Griggio F, Mastrototaro F, Delsuc F, Douzery EJ, Gissi C, Huchon D. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes. Genome Biol Evol 2013; 5:1185-99. [PMID: 23709623 PMCID: PMC3698926 DOI: 10.1093/gbe/evt081] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.
Collapse
Affiliation(s)
- Nimrod D. Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- Present address: Department of Molecular and Cellular Biology, Harvard University
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- The Steinhardt National Collections of Natural History Tel Aviv University, Ramat Aviv, Israel
| | - Noa Shenkar
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Fidel Botero-Castro
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | | | | | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Emmanuel J.P. Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Carmela Gissi
- Dip. di Bioscienze, Università degli Studi di Milano, Milano, Italy
- *Corresponding authors: E-mail: ;
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- *Corresponding authors: E-mail: ;
| |
Collapse
|
26
|
Meiri M, Huchon D, Bar-Oz G, Boaretto E, Horwitz LK, Maeir AM, Sapir-Hen L, Larson G, Weiner S, Finkelstein I. Ancient DNA and population turnover in southern levantine pigs--signature of the sea peoples migration? Sci Rep 2013; 3:3035. [PMID: 24186332 PMCID: PMC3816294 DOI: 10.1038/srep03035] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/23/2013] [Indexed: 11/20/2022] Open
Abstract
Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.
Collapse
Affiliation(s)
- Meirav Meiri
- 1] Institute of Archaeology, Tel Aviv University, Tel Aviv 69978, Israel [2] Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Szitenberg A, Becking LE, Vargas S, Fernandez JCC, Santodomingo N, Wörheide G, Ilan M, Kelly M, Huchon D. Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers. Mol Phylogenet Evol 2013; 67:509-19. [PMID: 23485919 DOI: 10.1016/j.ympev.2013.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 12/29/2012] [Accepted: 02/15/2013] [Indexed: 10/27/2022]
Abstract
Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
Collapse
Affiliation(s)
- Amir Szitenberg
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Belinky F, Szitenberg A, Goldfarb I, Feldstein T, Wörheide G, Ilan M, Huchon D. ALG11 – A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene. Mol Phylogenet Evol 2012; 63:702-13. [DOI: 10.1016/j.ympev.2012.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 11/30/2022]
|
29
|
Szitenberg A, Goren M, Huchon D. Mitochondrial and morphological variation of Tilapia zillii in Israel. BMC Res Notes 2012; 5:172. [PMID: 22469095 PMCID: PMC3412729 DOI: 10.1186/1756-0500-5-172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tilapia zillii is widespread in the East Levant inland aquatic systems as well as in artificial water reservoirs. In this study we explore the genetic and morphological variation of this widespread species, using mitochondrial control region sequences and meristic characters. We examine the hypothesis that T. zillii's population structure corresponds to the four Israeli aquatic systems. RESULTS Out of seven natural water bodies, only two were found to possess genetically divergent populations of T. zillii. In addition to its presence in fish farms, the species was found in two artificial recreational ponds which were supposed to have been stocked only with other fish species. In these two artificial habitats, the haplotype frequencies diverged significantly from those of natural populations. Finally, fish from the Dead Sea springs of Ne'ot HaKikar appear to differ both genetically and morphologically from fish of the same aquatic system but not from fish of other water systems. CONCLUSIONS Our results show that the population structure of T. zillii does not match the geography of the Israeli water-basins, with the exception of the Dead Sea and Kishon River, when considering natural populations only. The absence of a significant divergence between basins is discussed. Our results and observations suggest that the Ne'ot HaKikar Dead Sea population and those of artificial ponds could have originated from the "hitchhiking" of T. zillii, at the expense of some other cultivated tilapiine species.
Collapse
Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv, Israel
| | | | | |
Collapse
|
30
|
Abstract
UNLABELLED The evolutionary analysis of presence and absence profiles (phyletic patterns) is widely used in biology. It is assumed that the observed phyletic pattern is the result of gain and loss dynamics along a phylogenetic tree. Examples of characters that are represented by phyletic patterns include restriction sites, gene families, introns and indels, to name a few. Here, we present a user-friendly web server that accurately infers branch-specific and site-specific gain and loss events. The novel inference methodology is based on a stochastic mapping approach utilizing models that reliably capture the underlying evolutionary processes. A variety of features are available including the ability to analyze the data with various evolutionary models, to infer gain and loss events using either stochastic mapping or maximum parsimony, and to estimate gain and loss rates for each character analyzed. AVAILABILITY Freely available for use at http://gloome.tau.ac.il/.
Collapse
Affiliation(s)
- Ofir Cohen
- Department of Cell Research and Immunology, Tel-Aviv University, Tel Aviv 69978, Israel
| | | | | | | | | |
Collapse
|
31
|
Szitenberg A, Rot C, Ilan M, Huchon D. Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae. BMC Evol Biol 2010; 10:288. [PMID: 20849667 PMCID: PMC2955029 DOI: 10.1186/1471-2148-10-288] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/20/2010] [Indexed: 01/31/2023] Open
Abstract
Background Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family. Results Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant. Conclusions The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the cox 1 topologies. In addition, our results suggest that three different intron forms independently colonized the cox 1 gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.
Collapse
Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv 69978, Israel
| | | | | | | |
Collapse
|
32
|
Diamant A, Goren M, Yokeş MB, Galil BS, Klopman Y, Huchon D, Szitenberg A, Karhan SU. Dasyatispora levantinae gen. et sp. nov., a new microsporidian parasite from the common stingray Dasyatis pastinaca in the eastern Mediterranean. Dis Aquat Organ 2010; 91:137-150. [PMID: 21387993 DOI: 10.3354/dao02256] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new microsporidian infecting the Mediterranean common stingray Dasyatis pastinaca (Linnaeus, 1758) is described from Iskenderun Bay, Turkey. The parasite invades the disc muscles, producing slender, spindle-shaped subcutaneous swellings that develop into massive, elongated, tumor-like protuberances measuring up to 11 x 4 cm. Severity of the infection may vary from light (1 or 2 small lesions) to intense, with large parts of the dorsal surface covered with lumps and protrusions. These masses contained a yellowish-white caseous substance consisting of degraded host tissue and microsporidian sporophorous vesicles, which in turn contained developing sporonts, sporoblasts and spores. The ripe spore contained a uni-nucleate sporoplasm and large posterior vacuole, and measured 3.8-4.3 x 2.6-2.8 microm. Infection prevalence was 21% in a sample of 143 host individuals examined. All the infected stingray individuals were within the weight class of 300 to 800 g (200 to 305 mm disc width). Phylogenetic analyses of rDNA sequences indicate that this microsporidian belongs to the Pleistophoridae and clusters with species of the genera Ovipleistophora Pekkarinen, Lom & Nilsen, 2002 and Heterosporis Schubert, 1969. However, the morphology, development and host differ distinctly from all reported species, including those belonging to these 2 genera, and it is thus assigned to a newly erected genus and named Dasyatispora levantinae gen. et sp. nov. This is the first record of a microsporidian infection in a batoid. It is also the first microsporidian species to be formally described from an elasmobranch.
Collapse
Affiliation(s)
- Ariel Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, P.O.B. 1212, Eilat 88112, Israel.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
|
34
|
Singh TR, Tsagkogeorga G, Delsuc F, Blanquart S, Shenkar N, Loya Y, Douzery EJ, Huchon D. Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny. BMC Genomics 2009; 10:534. [PMID: 19922605 PMCID: PMC2785839 DOI: 10.1186/1471-2164-10-534] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 11/17/2009] [Indexed: 11/30/2022] Open
Abstract
Background Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. Results In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. Conclusion This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny.
Collapse
Affiliation(s)
- Tiratha Raj Singh
- Department of Zoology, George S Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
Insertions and deletions (indels) are considered to be rare evolutionary events, the analysis of which may resolve controversial phylogenetic relationships. Indeed, indel characters are often assumed to be less homoplastic than amino acid and nucleotide substitutions and, consequently, more reliable markers for phylogenetic reconstruction. In this study, we analyzed indels from over 1,000 metazoan orthologous genes. We studied the impact of different species sampling, ortholog data sets, lengths of included indels, and indel-coding methods on the resulting metazoan tree. Our results show that, similar to sequence substitutions, indels are homoplastic characters, and their analysis is sensitive to the long-branch attraction artifact. Furthermore, improving the taxon sampling and choosing a closely related outgroup greatly impact the phylogenetic inference. Our indel-based inferences support the Ecdysozoa hypothesis over the Coelomata hypothesis and suggest that sponges are a sister clade to other animals.
Collapse
|
36
|
Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJP, Delsuc F. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models. BMC Evol Biol 2009; 9:187. [PMID: 19656395 PMCID: PMC2739199 DOI: 10.1186/1471-2148-9-187] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 08/05/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. RESULTS Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. CONCLUSION An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.
Collapse
Affiliation(s)
- Georgia Tsagkogeorga
- Université Montpellier 2, Institut des Sciences de l'Evolution (UMR 5554), CC064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Shemesh E, Huchon D, Simon-Blecher N, Achituv Y. The distribution and molecular diversity of the Eastern Atlantic and Mediterranean chthamalids (Crustacea, Cirripedia). ZOOL SCR 2009. [DOI: 10.1111/j.1463-6409.2008.00384.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
38
|
Blanga-Kanfi S, Miranda H, Penn O, Pupko T, DeBry RW, Huchon D. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol 2009; 9:71. [PMID: 19341461 PMCID: PMC2674048 DOI: 10.1186/1471-2148-9-71] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 04/02/2009] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. RESULTS We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. CONCLUSION Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.
Collapse
Affiliation(s)
- Shani Blanga-Kanfi
- Department of Zoology, George S, Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.
| | | | | | | | | | | |
Collapse
|
39
|
Levin E, Yom-Tov Y, Barnea A, Huchon D. Genetic diversity and phylogeography of the greater mouse-tailed bat Rhinopoma microphyllum (Brünnich, 1782) in the Levant. Acta Chiropterologica 2008. [DOI: 10.3161/150811008x414791] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
40
|
Abstract
Two main gene orders exist in birds: the ancestral gene order and the remnant control region (CR) 2 gene order. These gene orders differ by the presence of 1 or 2 copies of the CR, respectively. Among songbirds, Oscines were thought to follow the ancestral gene order, with the exception of the lyrebird and Phylloscopus warblers. Here, we determined the complete mitochondrial genome sequence of 3 non-Phylloscopus warblers species and found that the blackcap (Sylvia atricapilla) and the reed warbler (Acrocephalus scirpaceus) have 2 almost identical copies of the CR, whereas the eastern orphean warbler (Sylvia crassirostris) follows the remnant CR 2 gene order. Our results contradict previous studies suggesting that Acrocephalus and most sylvioid warblers exhibit the ancestral gene order. We were able to trace this contradiction to a misidentification of gene order from polymerase chain reaction length determination. We thus suggest that passerine gene order evolution needs to be revised.
Collapse
|
41
|
Simon-Blecher N, Huchon D, Achituv Y. Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis. Mol Phylogenet Evol 2007; 44:1333-41. [PMID: 17560131 DOI: 10.1016/j.ympev.2007.03.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 03/08/2007] [Accepted: 03/29/2007] [Indexed: 11/24/2022]
Abstract
The traditional phylogeny of the coral-inhabiting barnacles, the Pyrgomatidae, is based on morphological characteristics, mainly of the hard parts. It has been difficult to establish the phylogenetic relationships among Pyrgomatidae because of the apparent convergence of morphological characteristics, and due to the use of non-cladistic systematics, which emphasize ancestor-descendant relationships rather than sister-clade relationships. We used partial sequences of two mithochondrial genes, 12S rDNA and 16S rDNA, and a nuclear gene, 18S rDNA, to infer the molecular phylogeny of the pyrgomatids. Our phylogenetic results allowed us to reject previous classifications of Pyrgomatidae based on morphological characteristics. Our results also suggested the possibility of paraphyly of the Pyrgomatidae. The hydrocoral barnacle Wanella is not found on the same clade as the other pyrgomatids, but rather, with the free-living balanids. The basal position of Megatrema and Ceratoconcha is supported. The archeaobalanid Armatobalanus is grouped with Cantellius at the base of the Indo-Pacific pyrgomatines. Fusion of the shell plate and modification of the opercular valves are homoplasious features that occurred more than three times on different clades. The monophyly of the "Savignium" group, comprising four nominal genera, is also not supported, and the different taxa are placed on different clades.
Collapse
MESH Headings
- Animals
- Anthozoa
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- DNA, Ribosomal/genetics
- Evolution, Molecular
- Genes, Mitochondrial
- Likelihood Functions
- Models, Genetic
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Symbiosis
- Thoracica/classification
- Thoracica/genetics
Collapse
Affiliation(s)
- N Simon-Blecher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | | | | |
Collapse
|
42
|
Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, Jenkins PD, Brosius J, Schmitz J. Multiple molecular evidences for a living mammalian fossil. Proc Natl Acad Sci U S A 2007; 104:7495-9. [PMID: 17452635 PMCID: PMC1863447 DOI: 10.1073/pnas.0701289104] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2007] [Indexed: 11/18/2022] Open
Abstract
Laonastes aenigmamus is an enigmatic rodent first described in 2005. Molecular and morphological data suggested that it is the sole representative of a new mammalian family, the Laonastidae, and a member of the Hystricognathi. However, the validity of this family is controversial because fossil-based phylogenetic analyses suggest that Laonastes is a surviving member of the Diatomyidae, a family considered to have been extinct for 11 million years. According to these data, Laonastes and Diatomyidae are the sister clade of extant Ctenodactylidae (i.e., gundies) and do not belong to the Hystricognathi. To solve the phylogenetic position of Laonastes, we conducted a large-scale molecular phylogeny of rodents. The analysis includes representatives of all major rodent taxonomic groups and was based on 5.5 kb of sequence data from four nuclear and two mitochondrial genes. To further validate the obtained results, a short interspersed element insertion analysis including 11 informative loci was also performed. Our molecular data based on sequence and short interspersed element analyses unambiguously placed Laonastes as a sister clade of gundies. All alternative hypotheses were significantly rejected based on Shimodaira-Hasegawa tests, supporting the idea that Laonastes does not belong to the Hystricognathi. Molecular dating analysis also supports an ancient divergence, approximately 44 Mya ago, between Ctenodactylidae and Laonastes. These combined analyses support the hypothesis that Laonastes is indeed a living fossil. Protection of this surviving species would conserve an ancient mammalian family.
Collapse
Affiliation(s)
- Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Pascale Chevret
- Department of Paleontology, Phylogeny, and Paleobiology, Institut des Sciences de l'Evolution, cc064, Université Montpellier II, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Ursula Jordan
- Institute of Experimental Pathology, University of Münster, D-48149 Münster, Germany
| | | | - Vincent Ranwez
- Department of Paleontology, Phylogeny, and Paleobiology, Institut des Sciences de l'Evolution, cc064, Université Montpellier II, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Paulina D. Jenkins
- Department of Zoology, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Jürgen Brosius
- Institute of Experimental Pathology, University of Münster, D-48149 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology, University of Münster, D-48149 Münster, Germany
| |
Collapse
|
43
|
Farwick A, Jordan U, Fuellen G, Huchon D, Catzeflis F, Brosius J, Schmitz J. Automated scanning for phylogenetically informative transposed elements in rodents. Syst Biol 2007; 55:936-48. [PMID: 17345675 DOI: 10.1080/10635150601064806] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Transposed elements constitute an attractive, useful source of phylogenetic markers to elucidate the evolutionary history of their hosts. Frequent and successive amplifications over evolutionary time are important requirements for utilizing their presence or absence as landmarks of evolution. Although transposed elements are well distributed in rodent taxa, the generally high degree of genomic sequence divergence among species complicates our access to presence/absence data. With this in mind we developed a novel, high-throughput computational strategy, called CPAL (Conserved Presence/Absence Locus-finder), to identify genome-wide distributed, phylogenetically informative transposed elements flanked by highly conserved regions. From a total of 232 extracted chromosomal mouse loci we randomly selected 14 of these plus 2 others from previous test screens and attempted to amplify them via PCR in representative rodent species. All loci were amplifiable and ultimately contributed 31 phylogenetically informative markers distributed throughout the major groups of Rodentia.
Collapse
Affiliation(s)
- Astrid Farwick
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
| | | | | | | | | | | | | |
Collapse
|
44
|
Rot C, Goldfarb I, Ilan M, Huchon D. Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. BMC Evol Biol 2006; 6:71. [PMID: 16972986 PMCID: PMC1618405 DOI: 10.1186/1471-2148-6-71] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Accepted: 09/14/2006] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera). RESULTS A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor. CONCLUSION Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.
Collapse
Affiliation(s)
- Chagai Rot
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Itay Goldfarb
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| |
Collapse
|
45
|
Abstract
Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the same molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and combined) from 60 species, and eight fossil calibration constraints, we estimated the times of origin and diversification of platyrrhines and caviomorphs via a Bayesian relaxed molecular clock approach. To account for the possible effect of an accelerated rate of evolution of the IRBP gene along the branch leading to the anthropoids, we performed the datings with and without IRBP (3768 sites and 2469 sites, respectively). The time window for the colonization of South America by primates and by rodents is demarcated by the dates of origin (upper bound) and radiation (lower bound) of platyrrhines and caviomorphs. According to this approach, platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of a concomitant arrival of primates and rodents in South America. The caviomorphs radiated soon after their arrival, before the Oligocene glaciations, and these early caviomorph lineages persisted until the present. By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification.
Collapse
Affiliation(s)
- Céline Poux
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie, CC064, Institut des Sciences de l'Evolution (UMR 5554/CNRS), Université Montpellier II, Place E., Bataillon, 34 095, Montpellier Cedex 05, France
| | | | | | | | | |
Collapse
|
46
|
Abstract
Phylogenetic analyses of 16S rRNA sequences of sponge-associated cyanobacteria showed them to be polyphyletic, implying that they derived from multiple independent symbiotic events. Most of the symbiont sequences were affiliated to a group of Synechococcus and Prochlorococcus species. However, other symbionts were related to different groups, such as the Oscillatoriales.
Collapse
Affiliation(s)
- Laura Steindler
- Department of Plant Sciences, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | | | | | | |
Collapse
|
47
|
Abstract
Rodentia (e.g., mice, rats, dormice, squirrels, and guinea pigs) and Lagomorpha (e.g., rabbits, hares, and pikas) are usually grouped into the Glires. Status of this controversial superorder has been evaluated using morphology, paleontology, and mitochondrial plus nuclear DNA sequences. This growing corpus of data has been favoring the monophyly of Glires. Recently, Misawa and Janke [Mol. Phylogenet. Evol. 28 (2003) 320] analyzed the 6441 amino acids of 20 nuclear proteins for six placental mammals (rat, mouse, rabbit, human, cattle, and dog) and two outgroups (chicken and xenopus), and observed a basal position of the two murine rodents among the former. They concluded that "the Glires hypothesis was rejected." We here reanalyzed [loc. cit.] data set under maximum likelihood and Bayesian tree-building approaches, using phylogenetic models that take into account among-site variation in evolutionary rates and branch-length variation among proteins. Our observations support both the association of rodents and lagomorphs and the monophyly of Euarchontoglires (=Supraprimates) as the most likely explanation of the protein alignments. We conducted simulation studies to evaluate the appropriateness of lissamphibian and avian outgroups to root the placental tree. When the outgroup-to-ingroup evolutionary distance increases, maximum parsimony roots the topology along the long Mus-Rattus branch. Maximum likelihood, in contrast, roots the topology along different branches as a function of their length. Maximum likelihood appears less sensitive to the "long-branch attraction artifact" than is parsimony. Our phylogenetic conclusions were confirmed by the analysis of a different protein data set using a similar sample of species but different outgroups. We also tested the effect of the addition of afrotherian and xenarthran taxa. Using the linearized tree method, [loc. cit.] estimated that mice and rats diverged about 35 million years ago. Molecular dating based on the Bayesian relaxed molecular clock method suggests that the 95% credibility interval for the split between mice and rats is 7-17 Mya. We here emphasize the need for appropriate models of sequence evolution (matrices of amino acid replacement, taking into account among-site rate variation, and independent parameters across independent protein partitions) and for a taxonomically broad sample, and conclude on the likelihood that rodents and lagomorphs together constitute a monophyletic group (Glires).
Collapse
Affiliation(s)
- Emmanuel J P Douzery
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie, CC064, Institut des Sciences de l'Evolution UMR 5554/CNRS, Université Montpellier II; Place E. Bataillon, 34 095 Montpellier Cedex 05, France.
| | | |
Collapse
|
48
|
Douzery EJP, Delsuc F, Stanhope MJ, Huchon D. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J Mol Evol 2004; 57 Suppl 1:S201-13. [PMID: 15008417 DOI: 10.1007/s00239-003-0028-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
Collapse
Affiliation(s)
- Emmanuel J P Douzery
- Laboratoire de Paléontologie, Paléobiologie et Phylogenie-CC064, Institut des Sciences de l'Evolution UMR 5554/CNRS, Université Montpellier II, Place E. Bataillon, 34 095 Montpellier Cedex 05, France.
| | | | | | | |
Collapse
|
49
|
|
50
|
Abstract
Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular data sets. Here, we compare several models for combining different genes for the purpose of evaluating the likelihood of tree topologies. Three methods of branch length estimation were studied: assuming all genes have the same branch lengths (concatenate model), assuming that branch lengths are proportional among genes (proportional model), or assuming that each gene has a separate set of branch lengths (separate model). We also compared three models of among-site rate variation: the homogenous model, a model that assumes one gamma parameter for all genes, and a model that assumes one gamma parameter for each gene. On the basis of two nuclear and one mitochondrial amino acid data sets, our results suggest that, depending on the data set chosen, either the separate model or the proportional model represents the most appropriate method for branch length analysis. For all the data sets examined, one gamma parameter for each gene represents the best model for among-site rate variation. Using these models we analyzed alternative mammalian tree topologies, and we describe the effect of the assumed model on the maximum likelihood tree. We show that the choice of the model has an impact on the best phylogeny obtained.
Collapse
Affiliation(s)
- Tal Pupko
- The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan.
| | | | | | | | | |
Collapse
|