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Ling MK, Yap NWL, Iesa IB, Yip ZT, Huang D, Quek ZBR. Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes. iScience 2023; 26:108252. [PMID: 37965150 PMCID: PMC10641506 DOI: 10.1016/j.isci.2023.108252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.
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Affiliation(s)
- Min Kang Ling
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Nicholas Wei Liang Yap
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- St. John’s Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Iffah Binte Iesa
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zhi Ting Yip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
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2
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Randolph Quek ZB, Jain SS, Richards ZT, Arrigoni R, Benzoni F, Hoeksema BW, Carvajal JI, Wilson NG, Baird AH, Kitahara MV, Seiblitz IGL, Vaga CF, Huang D. A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia). Mol Phylogenet Evol 2023:107867. [PMID: 37348770 DOI: 10.1016/j.ympev.2023.107867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.
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Affiliation(s)
- Z B Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.
| | - Sudhanshi S Jain
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia; Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms, Genoa Marine Centre, Stazione Zoologica Anton Dohrn-National Institute of Marine Biology, Ecology and Biotechnology, 16126 Genoa, Italy
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Bert W Hoeksema
- Taxonomy, Systematics and Geodiversity Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
| | - Jose I Carvajal
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Nerida G Wilson
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Andrew H Baird
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Marcelo V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, United States of America
| | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Claudia F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore.
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3
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Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
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Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Liu J, Yang Y, Yan Z, Wang H, Bai M, Shi C, Li J. Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera). BIOLOGY 2023; 12:biology12010135. [PMID: 36671827 PMCID: PMC9855730 DOI: 10.3390/biology12010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
Helotid beetles are commonly found in places where sap flows from tree trunks and in crevices in bark. The Helotidae family is a rare and primitive group of Cucujoidea. To date, no complete mitochondrial (mt) genome has been sequenced for this family. To better understand the characteristics of the mt genome and the evolution of Cucujoidea, we sequenced and annotated the complete mt genomes of Helota thoracica (Ritsema, 1895) and Helota yehi Lee, 2017 using next-generation sequencing. These are the first record of Helotidae mt genomes. The RNA secondary structures of both species were also predicted in this study. The mt genomes of H. thoracica and H. yehi are circular, with total lengths of 16,112 bp and 16,401 bp, respectively. After comparing the mt genomes of H. thoracica and H. yehi, we observed the gene arrangement, codon usage patterns, base content, and RNA secondary structures of both species to be similar, which has also been noted in other Coleoptera insects. The nucleotide sequence of the coding regions and the control region has small differences. The phylogenetic analysis indicated that Helotidae and Protocucujidae are sister groups and revealed the relationship between seven families; however, the validity of the two series (Erotylid series and Nitidulid series) as larger groups in the superfamily was not supported. The mt phylogenomic relationships have strong statistical support. Therefore, the division of Cucujoidea into series should be re-examined. Our results will provide a better understanding of the mt genome and phylogeny of Helotidae and Cucujoidea and will provide valuable molecular markers for further genetic studies.
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Affiliation(s)
- Jing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Yuhang Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Zihan Yan
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Haishan Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Ming Bai
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (M.B.); (J.L.)
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jing Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Correspondence: (M.B.); (J.L.)
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Park E, Poulin R. Extremely divergent COI sequences within an amphipod species complex: A possible role for endosymbionts? Ecol Evol 2022; 12:e9448. [PMID: 36311398 PMCID: PMC9609454 DOI: 10.1002/ece3.9448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Some heritable endosymbionts can affect host mtDNA evolution in various ways. Amphipods host diverse endosymbionts, but whether their mtDNA has been influenced by these endosymbionts has yet to be considered. Here, we investigated the role of endosymbionts (microsporidians and Rickettsia) in explaining highly divergent COI sequences in Paracalliope fluviatilis species complex, the most common freshwater amphipods in New Zealand. We first contrasted phylogeographic patterns using COI, ITS, and 28S sequences. While molecular species delimitation methods based on 28S sequences supported 3-4 potential species (N, C, SA, and SB) among freshwater lineages, COI sequences supported 17-27 putative species reflecting high inter-population divergence. The deep divergence between NC and S lineages (~20%; 28S) and the substitution saturation on the 3rd codon position of COI detected even within one lineage (SA) indicate a very high level of morphological stasis. Interestingly, individuals infected and uninfected by Rickettsia comprised divergent COI lineages in one of four populations tested, suggesting a potential influence of endosymbionts in mtDNA patterns. We propose several plausible explanations for divergent COI lineages, although they would need further testing with multiple lines of evidence. Lastly, due to common morphological stasis and the presence of endosymbionts, phylogeographic patterns of amphipods based on mtDNA should be interpreted with caution.
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Affiliation(s)
- Eunji Park
- Department of ZoologyUniversity of OtagoDunedinNew Zealand,Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Robert Poulin
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). Genetica 2022; 150:247-262. [PMID: 36083388 DOI: 10.1007/s10709-022-00165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.
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Chen L, Jin WT, Liu XQ, Wang XQ. New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data. Mol Phylogenet Evol 2021; 166:107341. [PMID: 34740782 DOI: 10.1016/j.ympev.2021.107341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.
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Affiliation(s)
- Luo Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin-Quan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Macher JN, Kayal E, Duijm E, van der Hoorn B, Montano S, Speksnijder A. The mitochondrial genome of Nemalecium lighti (Hydrozoa, Leptothecata). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3196-3198. [PMID: 34660901 PMCID: PMC8519520 DOI: 10.1080/23802359.2021.1989335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The hydrozoan species Nemalecium lighti (Hargitt, 1924) is widely distributed in tropical marine waters around the world. Here we report the complete linear mitochondrial genome of N. lighti from Sint Eustatius (Lesser Antilles). The mitochondrial genome with a length of 14,320 bp encodes for 13 protein-coding genes, two tRNA genes, and two rRNA genes. Gene arrangement differs from that found in other species of the same taxonomic order and a phylogenetic analysis shows that based on mitochondrial genes, N. lighti clusters outside of the Leptothecata, rendering the order paraphyletic.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Ehsan Kayal
- Université de Caen Normandie, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Caen, France
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Berry van der Hoorn
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,Inholland University of Applied Sciences, Delft, The Netherlands
| | - Simone Montano
- University of Milano-Bicocca, Department of Earth and Environmental Sciences (DISAT), Milano, Italy
| | - Arjen Speksnijder
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,University of Applied Sciences Leiden, Leiden, The Netherlands
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Terraneo TI, Benzoni F, Arrigoni R, Baird AH, Mariappan KG, Forsman ZH, Wooster MK, Bouwmeester J, Marshell A, Berumen ML. Phylogenomics of Porites from the Arabian Peninsula. Mol Phylogenet Evol 2021; 161:107173. [PMID: 33813021 DOI: 10.1016/j.ympev.2021.107173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia.
| | - Francesca Benzoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Roberto Arrigoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; European Commission, Joint Research Centre (JRC), Ispra, Italy; Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Napoli, Italy
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zac H Forsman
- Hawaii Institute of Marine Biology, Kaneohe 96744, HI, USA
| | - Michael K Wooster
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Michael L Berumen
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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10
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Seiblitz IGL, Capel KCC, Stolarski J, Quek ZBR, Huang D, Kitahara MV. The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. Sci Rep 2020; 10:20714. [PMID: 33244171 PMCID: PMC7693180 DOI: 10.1038/s41598-020-77763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/11/2020] [Indexed: 11/08/2022] Open
Abstract
Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
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Affiliation(s)
- Isabela G L Seiblitz
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
| | - Kátia C C Capel
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | | | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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11
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Gusmão LC, Van Deusen V, Daly M, Rodríguez E. Origin and evolution of the symbiosis between sea anemones (Cnidaria, Anthozoa, Actiniaria) and hermit crabs, with additional notes on anemone-gastropod associations. Mol Phylogenet Evol 2020; 148:106805. [PMID: 32217169 DOI: 10.1016/j.ympev.2020.106805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/10/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022]
Abstract
The anemone-crab mutualism is ubiquitous in temperate and tropical marine environments. In this symbiosis, one or more anemones live on a shell inhabited by a hermit crab and reciprocal phoretic, trophic, and defensive benefits are exchanged between the partners. Sea anemone-hermit crab symbionts belong to three families: Hormathiidae (Calliactis and Paracalliactis), Sagartiidae (Carcinactis and Verrillactis), and Actiniidae (Stylobates). Hermit crabs establish most partnerships by detaching anemones and placing them on their shell; sea anemones can also mount shells unaided, triggered by a mollusc-derived substance in the periostracum of the shell. At least partial cooperation by the anemones is necessary for successful establishment of the symbiosis. Here, we expand the evolutionary framework for hormathiid symbionts by generating a phylogeny with at least one member of each actiniarian symbiotic genus with hermit crabs using five molecular markers (16S, 12S, 18S, 28S, CO3). We not only corroborated the results from a previous study by finding two origins of hermit crab symbiosis within Hormathiidae, but also found additional origins for hermit crab symbiosis within Actiniaria. We provide for the first time evidence of a close relationship between symbionts Carcinactis dolosa and V. paguri. The ability to secrete chitin by the ectoderm of the column is inferred to be broadly convergent within Actiniaria whereas the secretion of a chitinous carcinoecium by the pedal disc is a distinct but convergent morphological adaptation of several lineages within Actiniaria. Our finding of multiple origins for both the hermit crab and gastropod symbioses suggests that the shell-mounting behavior might only have been the precursor of the hermit crab association among Calliactis spp.
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Affiliation(s)
- Luciana C Gusmão
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
| | - Vanessa Van Deusen
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA; Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Museum of Biological Diversity, 1315 Kinnear Road, Columbus, OH 43212, USA.
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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12
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Hancy AD, Antcliffe JB. Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record. GEOBIOLOGY 2020; 18:167-184. [PMID: 31990129 DOI: 10.1111/gbi.12370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).
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Affiliation(s)
- Anthony D Hancy
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Jonathan B Antcliffe
- Oxford University Museum of Natural History, Oxford, UK
- Institut des Sciences de la Terre, Bâtiment Géopolis, UNIL-Mouline, Université de Lausanne, Lausanne, Switzerland
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13
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Xiao M, Brugler MR, Broe MB, Gusmão LC, Daly M, Rodríguez E. Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria. Sci Rep 2019; 9:18182. [PMID: 31796816 PMCID: PMC6890759 DOI: 10.1038/s41598-019-54637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.
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Affiliation(s)
- Madelyne Xiao
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Mercer R Brugler
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Biological Sciences Department, NYC College of Technology (CUNY), 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA
| | - Luciana C Gusmão
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.
| | - Estefanía Rodríguez
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
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14
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Richards ZT, Carvajal JI, Wallace CC, Wilson NG. Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae. Mar Genomics 2019; 50:100703. [PMID: 31466869 DOI: 10.1016/j.margen.2019.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 01/17/2023]
Abstract
The genus Alveopora is a scleractinian coral taxon whose phylogenetic classification has recently changed from the family Poritidae to Acroporidae. This change, which was made based on single-locus genetic data, has led to uncertainty about the placement of Alveopora and the ability for deep evolutionary relationships in these groups to be accurately recovered and represented by limited genetic datasets. We sought to characterize the higher-level position of Alveopora using newly available transcriptome data to confirm its placement within Acroporidae and resolve its closest ancestor. Here we present an analysis of a new 2031 gene dataset that confirms the placement of Alveopora within Acroporidae corroborating other single-locus (COI, 16S and ITS) analyses and a mitogenome dataset. We also resolve the position of Alveopora as sister to the genus Montipora. This has allowed the re-interpretation of morphology, and a rediagnosis of the family Acroporidae and the genus Alveopora.
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Affiliation(s)
- Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6012, Australia; Department of Aquatic Zoology, Western Australian Museum, Kew Street, Welshpool, WA, 6106, Australia.
| | - Jose I Carvajal
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia
| | - Carden C Wallace
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, Queensland 4101, Australia
| | - Nerida G Wilson
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
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15
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
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16
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Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
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17
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Phylogenetic analysis of the mitochondrial genomes in bees (Hymenoptera: Apoidea: Anthophila). PLoS One 2018; 13:e0202187. [PMID: 30092091 PMCID: PMC6084986 DOI: 10.1371/journal.pone.0202187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022] Open
Abstract
In this study, the first complete mitogenome of Andrenidae, namely Andrena camellia, is newly sequenced. It includes 13 protein-coding (PCG) genes, 22 transfer RNA (rRNA) genes, two ribosomal RNA (tRNA) genes, and a control region. Among PCGs, high conservation is observed in cytochrome oxidase genes with cox1 exhibits the highest conservation. Conversely, NADH dehydrogenase and ATPase subunit genes are more variable with atp8 presents the maximal variation. Comparison of the gene order indicates complex rearrangement in bees. Most of the rearranged events are located in the tRNA clusters of trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Furthermore, we present the most comprehensive mitochondrial phylogeny of bee families. The monophyly of each family and the long-tongued bees is highly supported. However, short-tongued bees are inferred as paraphyletic relative to the sister relationship between Melittidae and other bee families. Furthermore, to improve the resolution of phylogeny, various datasets and analytical approaches are performed. It is indicated that datasets including third codons of PCGs facilitate to produce identical topology and higher nodal support. The tRNA genes that have typical cloverleaf secondary structures also exhibit similar positive effects. However, rRNAs present poor sequence alignment and distinct substitution saturation, which result in negative effects on both tree topology and nodal support. In addition, Gblocks treatment can increase the congruence of topologies, but has opposite effects on nodal support between the two inference methods of maximum likelihood and Bayesian inference.
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18
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Kayal E, Bentlage B, Sabrina Pankey M, Ohdera AH, Medina M, Plachetzki DC, Collins AG, Ryan JF. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evol Biol 2018. [PMCID: PMC5932825 DOI: 10.1186/s12862-018-1142-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including stinging cells, symbiosis, colonial body plans and elaborate life histories. However, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome-scale data for each major cnidarian lineage. Results Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome-scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and in the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Conclusions Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of some of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago. Electronic supplementary material The online version of this article (10.1186/s12862-018-1142-0) contains supplementary material, which is available to authorized users.
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19
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Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto‐Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis‐Baptista G, Ramírez‐Portilla C, Sánchez JA, Rodríguez E, McFadden CS. Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems. Mol Ecol Resour 2017; 18:281-295. [DOI: 10.1111/1755-0998.12736] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
| | - Luisa F. Dueñas
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Tom C. L. Bridge
- Queensland Museum Network Townsville QLD Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Mercer R. Brugler
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
- Biological Sciences Department NYC College of Technology City University of New York Brooklyn NY USA
| | - Iván F. Calixto‐Botía
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Danielle M. DeLeo
- Department of Biological Sciences Florida International University North Miami FL USA
- Biology Department Temple University Philadelphia PA USA
| | - Sylvain Forêt
- Research School of Biology Australian National University Canberra ACT Australia
| | - Santiago Herrera
- Department of Biological Sciences Lehigh University Bethlehem PA USA
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences University of Macau Macao China
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Carlos Prada
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | | | - Catalina Ramírez‐Portilla
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Juan A. Sánchez
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
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20
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Aurelle D, Pivotto ID, Malfant M, Topçu NE, Masmoudi MB, Chaoui L, Kara HM, Coelho MA, Castilho R, Haguenauer A. Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes. ZOOL SCR 2017. [DOI: 10.1111/zsc.12245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
| | - Isabelle D. Pivotto
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Department of Computer Science and Operations Research (DIRO); University of Montreal; Montréal QC 2194 Canada
| | - Marine Malfant
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Lab. « Adaptation et Diversité en Milieu Marin »; Team Div&Co; Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144; 29682 Roscoff France
| | - Nur E. Topçu
- Fisheries Faculty; Istanbul University; Ordu Cad No 200 34130 Laleli Istanbul Turkey
| | - Mauatassem B. Masmoudi
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Lamya Chaoui
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Hichem M. Kara
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Márcio A.G. Coelho
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
| | - Rita Castilho
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
- Graduate Program in Evolution, Ecology and Behavior; University at Buffalo; Buffalo NY 14260 USA
| | - Anne Haguenauer
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
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21
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28405374 DOI: 10.5061/dryad.rs7bm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A Haguenauer
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - S Chenesseau
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - K Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - G Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - E Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - M Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - S Rialle
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - D Aurelle
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - P Pontarotti
- Aix Marseille Univ , CNRS, Centrale Marseille, I2M , Marseille , France
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22
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017; 4:160880. [PMID: 28405374 PMCID: PMC5383831 DOI: 10.1098/rsos.160880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/01/2017] [Indexed: 05/29/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M. Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A. Haguenauer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - S. Chenesseau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - K. Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - G. Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - E. Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - M. Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - S. Rialle
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - D. Aurelle
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - P. Pontarotti
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
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