title: An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates.
abstract: Peritrichs are a major group of ciliates with worldwide distribution. Yet, its internal phylogeny remains unresolved owing to limited sampling. Additionally, ecological distributions of peritrichs are poorly known. We performed substantially expanded phylogenetic analyses of peritrichs that incorporated SSU rDNA sequences of samples collected from three continents, revealing a number of new relationships between and within major lineages that greatly challenged the classic view of the group. Interrogation of a dataset comprising new environmental sequences from an estuary and the open ocean generated with high throughput sequencing and clone libraries plus putative environmental peritrich sequences at Genbank, produced a comprehensive tree of peritrichs from a variety of habitats and revealed unique ecological distribution patterns of several lineages for the first time. Also, evidence of adaptation to extreme environments in the Astylozoidae clade greatly broadened the phylogenetic range of peritrichs capable of living in extreme environments. Reconstruction of ancestral states revealed that peritrichs may have transitioned repeatedly from freshwater to brackish/marine/hypersaline environments. This work establishes a phylogenetic framework for more mature investigations of peritrichs in the future, and the approach used here provides a model of how to elucidate evolution in the context of ecological niches in any lineage of microbial eukaryotes.
authors.affiliation: Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.|Fujian Province Key Laboratory for Coastal Ecology and Environmental studies, Xiamen University, Xiamen 361102, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Sun
authors.affiliation: Department of Biology, North Carolina Central University, Durham, NC 27707, USA.
authors.forename: John
authors.initials: J
authors.lastname: Clamp
authors.affiliation: State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Xu
authors.affiliation: Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.|Fujian Province Key Laboratory for Coastal Ecology and Environmental studies, Xiamen University, Xiamen 361102, China.
authors.forename: Bangqin
authors.initials: B
authors.lastname: Huang
authors.affiliation: Department of Biological Sciences, University of Ulsan, Ulsan 680-749, Korea.
authors.forename: Mann Kyoon
authors.initials: MK
authors.lastname: Shin
mesh_terms: D016798:Ciliophora / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D063366:Estuaries; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D009792:Oceans and Seas; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014871:Water Microbiology
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S