4.7 Article

ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene

期刊

MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 63, 期 3, 页码 702-713

出版社

ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2012.02.008

关键词

ALG11; COI; 18S rDNA; Porifera; Cnidaria; Molecular phylogeny; Saturation

资金

  1. Israeli Ministry of Science Culture Sport
  2. Israel Science Foundation [600/06]
  3. National Evolutionary Synthesis Center (NESCent), NSF [EF-0905606]
  4. German Science Foundation (DFG) [Wo896/6, 1-4]

向作者/读者索取更多资源

Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians. (c) 2012 Elsevier Inc. All rights reserved.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Chemistry, Medicinal

Theonellamides J and K and 5-cis-Apoa-theopalauamide, Bicyclic Glycopeptides of the Red Sea Sponge Theonella swinhoei

Ohad Hasin, Shani Shoham, Yoel Kashman, Micha Ilan, Shmuel Carmeli

Summary: This study analyzed the metabolites of Theonella swinhoei, a common inhabitant of reefs in the Indian and Pacific Oceans, collected at different depths. Two chemotypes of T. swinhoei were identified based on the profiles of the theonellamides they produce. Additionally, a sample of T. swinhoei collected over 40 years ago was analyzed, resulting in the discovery of three new metabolites. The structures of these complex cyclic glycopeptides were elucidated using various techniques, and their antibacterial and cytotoxic activities were evaluated.

MARINE DRUGS (2022)

Article Biochemistry & Molecular Biology

Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress

Sergio Vargas, Thorsten Zimmer, Nicola Conci, Martin Lehmann, Gert Woerheide

Summary: While many coral reef species are threatened by overfishing, some octocorals show resilience to anthropogenic environmental changes and may replace stony corals in the future. Research has found that the molecular mechanisms of octocorals, such as Pinnigorgia flava, exhibit resilience to heat and seawater acidification stress. This provides insights into their adaptive responses to anthropogenically driven environmental changes.

MOLECULAR ECOLOGY (2022)

Article Genetics & Heredity

Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea

Amir Szitenberg, Pedro Beca-Carretero, Tomas Azcarate-Garcia, Timur Yergaliyev, Rivka Alexander-Shani, Gidon Winters

Summary: This study investigated the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and phenological traits in Halophila stipulacea seagrass. The results showed that the source site of the seagrasses had a major impact on seagrass phenology, while bacterial diversity mainly depended on environmental conditions. Nutrient stress triggered an increase in Rhodobacteraceae and Microtrichaceae, which could potentially buffer nutrient concentrations on the leaf surface.

ENVIRONMENTAL MICROBIOME (2022)

Article Evolutionary Biology

The Phylogenetic Position of the Enigmatic, Polypodium hydriforme (Cnidaria, Polypodiozoa): Insights from Mitochondrial Genomes

Maria Novosolov, Dayana Yahalomi, E. Sally Chang, Ivan Fiala, Paulyn Cartwright, Dorothee Huchon

Summary: In this study, we analyzed the mitochondrial genome of Polypodium hydriforme and found that it is circular, contradicting the previous belief that it belongs to the phylum Medusozoa. Our results support the notion that P. hydriforme is closely related to Myxozoa and that the linearization of mitochondrial chromosomes in medusozoans occurred after the divergence of Myxozoa and P. hydriforme. Furthermore, the P. hydriforme mitochondrial genome is one of the largest among metazoan species and is characterized by rapid evolution.

GENOME BIOLOGY AND EVOLUTION (2022)

Article Multidisciplinary Sciences

Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee

Aditya Gupta, Michal Haddas-Sasson, Kfir Gayer, Dorothee Huchon

Summary: The economically important mullets in Israel have been stocked in the Sea of Galilee to increase income and water quality. A study found new species of myxozoan infections in the gill arches and reported infections in the visceral peritoneum and gall bladder of one species of mullet. The parasites may have been contracted in the Mediterranean Sea before introduction into the Sea of Galilee.

SCIENTIFIC REPORTS (2022)

Article Zoology

A new species of crown-of-thorns sea star, Acanthaster benziei sp. nov. (Valvatida: Acanthasteridae), from the Red Sea

Gert Woerheide, Emilie Kaltenbacher, Zara-Louise Cowan, Gerhard Haszprunar

Summary: A new species of crown-of-thorns sea star, Acanthaster benziei sp. nov., is described based on genetic and morphological analysis, distinguishing it from other similar species.

ZOOTAXA (2022)

Article Limnology

High variability and enhanced nocturnal oxygen uptake in coral reef sponges

Raz Moskovich, Rei Diga, Micha Ilan, Gitai Yahel

Summary: The in situ metabolism of sponges was examined by measuring the oxygen concentrations inhaled and exhaled by undisturbed sponges. The study found that there is a clear daily pattern of oxygen removal in sponges, with nocturnal removal being almost double the diurnal values. This diel difference in oxygen removal can be partially explained by photosynthesis, but other factors may also contribute.

LIMNOLOGY AND OCEANOGRAPHY (2023)

Article Chemistry, Medicinal

Seasonal Molecular Difference in Fibrillar Collagen Extracts Derived from the Marine Sponge Chondrosia reniformis (Nardo, 1847) and Their Impact on Its Derived Biomaterials

Eleonora Tassara, Boaz Orel, Micha Ilan, Dario Cavallo, Andrea Dodero, Maila Castellano, Silvia Vicini, Marco Giovine, Marina Pozzolini

Summary: This study investigates the molecular and chemical-physical properties of collagen extracted from Chondrosia reniformis sponges collected in different seasons to evaluate the potential impact of sea temperature. The results show that collagen fibrils extracted from samples at 17 degrees C have lower lysyl-hydroxylation level, thermal stability, and protein glycosylation level compared to those extracted from samples at 27 degrees C. Membranes made from 17 degrees C fibrils exhibit higher stiffness than those made from 27 degrees C fibrils. The differences in collagen properties are important in guiding the use of the biomaterial.

MARINE DRUGS (2023)

Article Paleontology

A new sponge genus from the Chengjiang biota with an intriguing combination of skeletal characters

Ailin Chen, Luis Porras, Haidan Ma, Xianguang Hou, Gert Woerheide

Summary: In this paper, we describe a new sponge with unique characteristics, indicating its relevance to the evolution of ancient sponges. This new taxon shows similarities to the total group of Silicea and a combination of filtering sponges, suggesting a potential connection between two major types of Early Palaeozoic sponge body plans. A more accurate definition of the Cambro-Ordovician groups and the creation of a total evidence framework that integrates extinct and extant sponge morphology into the phylogenetic scenario derived from phylogenomics seem to be essential steps for the improvement of our understanding of early sponge evolution.
Article Multidisciplinary Sciences

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

Ksenia Juravel, Luis Porras, Sebastian Hoehna, Davide Pisani, Gert Woerheide

Summary: An accurate understanding of the evolution and ecology of animals relies on an accurate phylogeny. However, there are still unresolved nodes in the animal tree, including the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. In this study, we utilized newly assembled genome gene content and morphological datasets to investigate these difficult nodes. Our results support the idea that sponges are the sister group of all other animals, Xenacoelomorpha is the sister group of other Bilateria, and provide tentative support for the monophyly of Deuterostomia.

PLOS ONE (2023)

Article Zoology

Genetic data confirms the enigmatic demosponge Janulum as haplosclerid

Dirk Erpenbeck, Rob W. M. Van Soest, Gert Woerheide, Michelle Kelly

ZOOTAXA (2023)

Article Environmental Sciences

A comparison of mesophotic and shallow sponge holobionts resilience to predicted future temperature elevation

Lilach Raijman-Nagar, Liron Goren, Sigal Shefer, Raz Moskovich, Zhiyong Li, Micha Ilan

Summary: Climate change negatively affects sponges, but the ability of mesophotic sponges to cope with heat stress is poorly understood. This study compared the response of Red Sea sponge Diacarnus erythraeanus from shallow and mesophotic reefs to moderate and acute heat stress. The results showed that both populations of D. erythraeanus were highly tolerant to heat stress but exhibited physiological and microbial changes, suggesting potential genetic variability between hosts.

FRONTIERS IN MARINE SCIENCE (2023)

Article Zoology

Revision of the genus Fascaplysinopsis, the type species Fascaplysinopsis reticulata (Hentschel, 1912) (Porifera, Dictyoceratida, Thorectidae) and descriptions of two new genera and seven new species

Merrick Ekins, Dirk Erpenbeck, Cecile Debitus, Sylvain Petek, Tepoerau Mai, Gert Woerheide, John N. A. Hooper

Summary: This study examines the taxonomy of sponge specimens with unique chemistry collectively known as Fascaplysinopsis reticulata. The results revealed that Fascaplysinopsis reticulata is a species complex comprising the genus Fascaplysinopsis, as well as two new genera: Skolosachlys gen. nov. and Rubrafasciculus gen. nov. Several new species were described within these genera.

ZOOTAXA (2023)

Article Biodiversity Conservation

Against the flow: Integrated taxonomy and environmental suitability of a cold-water species dispersing to warmer waters

Federica Montesanto, Racheli Hadjez, Francesco Mastrototaro, Dorothee Huchon, Carmela Gissi, Lion Novak, Noa Shenkar

Summary: The study describes the dispersal of the ascidian species Ascidia virginea from North Europe to warmer regions, highlighting the trend of species introduction through marine vessels and successful establishment in unfavorable environmental conditions. The research provides valuable data for species identification and habitat prediction, emphasizing the need to explore the potential of cold-water species in ports and warmer regions.

BIOLOGICAL INVASIONS (2023)

Article Zoology

Deep Water Polymastiidae (Porifera, Polymastiida) from the South West Pacific

Merrick Ekins, Dirk Erpenbeck, Gert Woerheide, John N. A. Hooper

Summary: This study reports on new deep water sponge species discovered in the East Coast of Australia and the Lord Howe and Norfolk Ridges in the Tasman Sea. In addition, two previously known species have been redescribed based on the new collections.

ZOOTAXA (2023)

Article Biochemistry & Molecular Biology

Paraphyly and cryptic diversity unveils unexpected challenges in the naked lichens (Calvitimela, Lecanoromycetes, Ascomycota)

Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby

Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China

Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun

Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko

Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda

Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun

Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections

Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan

Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean

Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling

Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)

Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu

Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes)

Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson

Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Hyper-Cryptic radiation of a tropical montane plant lineage

Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris

Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)