1
|
Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
Collapse
Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
2
|
Hao CL, Wei NW, Liu YJ, Shi CX, Arken K, Yue C. Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic. Parasit Vectors 2023; 16:83. [PMID: 36859280 PMCID: PMC9979435 DOI: 10.1186/s13071-023-05692-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Unresolved taxonomic classification and paraphyly pervade the flatworm class Monogenea: the class itself may be paraphyletic and split into Polyopisthocotylea and Monopisthocotylea; there are some indications that the monopisthocotylean order Dactylogyridea may also be paraphyletic; single-gene markers and some morphological traits indicate that the family Ancyrocephalidae is paraphyletic and intertwined with the family Dactylogyridae. METHODS To attempt to study the relationships of Ancyrocephalidae and Monopisthocotylea using a phylogenetic marker with high resolution, we sequenced mitochondrial genomes of two fish ectoparasites from the family Dactylogyridae: Dactylogyrus simplex and Dactylogyrus tuba. We conducted phylogenetic analyses using three datasets and three methods. Datasets were ITS1 (nuclear) and nucleotide and amino acid sequences of almost complete mitogenomes of almost all available Monopisthocotylea mitogenomes. Methods were maximum likelihood (IQ-TREE), Bayesian inference (MrBayes) and CAT-GTR (PhyloBayes). RESULTS Both mitogenomes exhibited the ancestral gene order for Neodermata, and both were compact, with few and small intergenic regions and many and large overlaps. Gene sequences were remarkably divergent for nominally congeneric species, with only trnI exhibiting an identity value > 80%. Both mitogenomes had exceptionally low A + T base content and AT skews. We found evidence of pervasive compositional heterogeneity in the dataset and indications that base composition biases cause phylogenetic artefacts. All six mitogenomic analyses produced unique topologies, but all nine analyses produced topologies that rendered Ancyrocephalidae deeply paraphyletic. Mitogenomic data consistently resolved the order Capsalidea as nested within the Dactylogyridea. CONCLUSIONS The analyses indicate that taxonomic revisions are needed for multiple Polyopisthocotylea lineages, from genera to orders. In combination with previous findings, these results offer conclusive evidence that Ancyrocephalidae is a paraphyletic taxon. The most parsimonious solution to resolve this is to create a catch-all Dactylogyridae sensu lato clade comprising the current Ancyrocephalidae, Ancylodiscoididae, Pseudodactylogyridae and Dactylogyridae families, but the revision needs to be confirmed by another marker with a sufficient resolution.
Collapse
Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cai-Xia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China.
| |
Collapse
|
3
|
Hao CL, Arken K, Kadir M, Zhang WR, Rong MJ, Wei NW, Liu YJ, Yue C. Correction: The complete mitochondrial genomes of Paradiplozoon yarkandense and Paradiplozoon homoion confirm that Diplozoidae evolve at an elevated rate. Parasit Vectors 2022; 15:169. [PMID: 35578272 PMCID: PMC9112599 DOI: 10.1186/s13071-022-05308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Munira Kadir
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Wen-Run Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Meng-Jie Rong
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China.
| |
Collapse
|