title: Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists.
abstract: Ciliates comprise a highly diverse protozoan lineage inhabiting all biotopes and playing crucial roles in regulating microbial food webs. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. Here, we use the species-rich taxon Frontonia and employ both nuclear and mitochondrial loci. We attempt to assess the level of genetic diversity and evaluate the potential of each marker in delineating species of Frontonia. Morphological features and ecological characteristics are also integrated into genetic results, in an attempt to resolve conflicts of species identification based on morphological and molecular methods. Our studies reveal: (1) the mitochondrial cox1 gene, nuclear ITS1 and ITS2 as well as the hypervariable D2 region of LSU rDNA are promising candidates for species delineation; (2) the cox1 gene provides the best resolution for analyses below the species level; (3) the V2 and V4 hypervariable regions of SSU rDNA, and D1 of LSU rDNA as well as the 5.8S rDNA gene do not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences; (4) morphological character-based analysis shows promise for delimitation of Frontonia species; and (5) all gene markers and character-based analyses demonstrate that the genus Frontonia consists of three groups and monophyly of the genus Frontonia is questionable.
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China(1).
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Science, South China Normal University, Guangzhou 510631, China. Electronic address: zyi@scnu.edu.cn.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Yi
authors.affiliation: School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.
authors.forename: Eleni
authors.initials: E
authors.lastname: Gentekaki
authors.affiliation: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China(1).
authors.forename: Aibin
authors.initials: A
authors.lastname: Zhan
authors.affiliation: Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
authors.forename: Saleh A
authors.initials: SA
authors.lastname: Al-Farraj
authors.affiliation: Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Song
mesh_terms: D002467:Cell Nucleus; D004275:DNA, Ribosomal; D050259:Genes, Mitochondrial; D005819:Genetic Markers; D014644:Genetic Variation; D058889:Molecular Typing; D016802:Oligohymenophorea / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D004275:DNA, Ribosomal; D005819:Genetic Markers
keywords: Ciliated protists; DNA-based taxonomy; Frontonia; Genetic distance; Morphological characters; Species identification