Abstract
Background
Anhinga melanogaster is a carnivorous water bird native to many Asian countries. A. melanogaster is part of the Old World clade of darters. There is currently significant debate about the organization of the Old World clade due to morphological and genetic ambiguities. It is essential to establish the taxonomic status of A. melanogaster because it was recently listed by the International Union for Conservation of Nature (IUCN) as a near threatened species.
Methods and results
The present study utilized a comprehensive molecular approach of the complete mitogenome of A. melanogaster to resolve its taxonomic status within the genus Anhinga. The mitogenome of A. melanogaster comprised of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. A partially duplicated cytochrome b gene and control region were also present.
Conclusions
Duplicated mitogenomic segments and phylogenetic analyses suggest that A. melanogaster, A. novaehollandiae, A. rufa and A. anhinga should be considered distinct species within the Old World clade of darters. The present study provides new insights into the mitogenome features of A. melanogaster and its evolutionary relationship within the genus, Anhinga.
Similar content being viewed by others
References
Harrison CJO (1978) Osteological differences in the leg bones of two forms of Anhinga. Emu 78:230–231. https://doi.org/10.1071/MU9780230
Johnsgard PA (1993) Cormorants, Darters, and Pelicans of the World. Smithsonian Institution Press, Washington
Worthy TH (2012) A new species of Oligo-Miocene darter (Aves: Anhingidae) from Australia. Auk 129:96–104. https://doi.org/10.1525/auk.2012.11204
Stidham T, Patnaik R, Krishan K, Singh B, Ghosh A, Singla A, Kotla SS (2017) The first darter (Aves: Anhingidae) fossils from India (late Pliocene). PloS one 12:e0177129. https://doi.org/10.1371/journal.pone.0177129
Kennedy M, Seneviratne SS, Mendis UK, Spencer HG (2019) Sorting out the snakebirds: The species status, phylogeny, and biogeography of the darters (Aves: Anhingidae). J Zool Syst Evol Res 57:892–899. https://doi.org/10.1111/jzs.12299
Schodde R, Kirwan GM, Porter R (2012) Morphological differentiation and speciation among darters (Anhinga). Bull Br Ornithol Club 132:283–294
Nagarajan M, Raja M, Vikram P (2016) Genetic characterization of Bagarius species using cytochrome c oxidase I and cytochrome b genes. Mitochondrial DNA Part A 27:3781–3783. https://doi.org/10.3109/19401736.2015.1079902
Kameshpandian P, Thomas S, Nagarajan M (2018) Genetic diversity and relationship of Indian Muscovy duck populations. Mitochondrial DNA Part A 29:165–169. https://doi.org/10.1080/24701394.2016.1261851
Kamalakkannan R, Jose J, Thomas S, Prabhu VR, Nagarajan M (2018) Genetic diversity and maternal lineages of south Indian goats. Mol Biol Rep 45:2741–2748. https://doi.org/10.1007/s11033-018-4322-5
Prabhu VR, Arjun MS, Bhavana K, Kamalakkannan R, Nagarajan M (2019) Complete mitochondrial genome of Indian mithun, Bos frontalis and its phylogenetic implications. Mol Biol Rep 46:2561–2566. https://doi.org/10.1007/s11033-019-04675-0
Prabhu VR, Singha HS, Kumar RG, Gopalakrishnan A, Nagarajan M (2020) Characterization of the complete mitochondrial genome of Barilius malabaricus and its phylogenetic implications. Genomics 112:2154–2163. https://doi.org/10.1016/j.ygeno.2019.12.009
Kamalakkannan R, Bhavana K, Prabhu VR, Sureshgopi D, Singha HS, Nagarajan M (2020) The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications. Sci Rep 10:1–11. https://doi.org/10.1038/s41598-020-68724-6
Kennedy M, Holland BR, Gray RD, Spencer HG (2005) Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst Biol 54:620–633. https://doi.org/10.1080/106351591007462
Sambrook J, Russell DW (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. https://doi.org/10.14806/ej.17.1.200
Joshi N, Fass J (2011) Sickle: A sliding-window, adaptive, quality-based trimming tool for fastQ files (version 1.33) [software]. Accessed https://github.com/najoshi/sickle
Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S (2012) FastUniq: a fast de novo duplicates removal tool for paired short reads. PloS one 7:e52249. https://doi.org/10.1371/journal.pone.0052249
Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–319. https://doi.org/10.1016/j.ympev.2012.08.023
Greiner S, Lehwark P, Bock R (2019) Organellar genome draw (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47:W59–W64. https://doi.org/10.1093/nar/gkz238
Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57. https://doi.org/10.1093/nar/gkw413
Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358. https://doi.org/10.1007/BF01215182
Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574
Cho HJ, Eda M, Nishida S, Yasukochi Y, Chong JR, Koike H (2009) Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor. Genes Genet Syst 84:297–305. https://doi.org/10.1266/ggs.84.297
Zhou X, Lin Q, Fang W, Chen X (2014) The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 15:1–9. https://doi.org/10.1186/1471-2164-15-573
Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D (2007) Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol Biol Evol 24:269–280. https://doi.org/10.1093/molbev/msl158
Morris-Pocock JA, Taylor SA, Birt TP, Friesen VL (2010) Concerted evolution of duplicated mitochondrial control regions in three related seabird species. BMC Evol Biol 10:14. https://doi.org/10.1186/1471-2148-10-14
San Mauro D, García-París M, Zardoya R (2004) Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343:357–366. https://doi.org/10.1016/j.gene.2004.10.001
Liu G, Li C, Du Y, Liu X (2017) The complete mitochondrial genome of Japanese sparrowhawk (Accipiter gularis) and the phylogenetic relationships among some predatory birds. Biochem Syst Ecol 70:116–125. https://doi.org/10.1016/j.bse.2016.11.007
Chen W, Zhang C, Pan T, Liu W, Li K, Hu C, Chang Q (2018) The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii. Genes Genom 40:955–963. https://doi.org/10.1007/s13258-018-0703-3
Eberhard JR, Wright TF, Bermingham E (2001) Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol Biol Evol 18:1330–1342. https://doi.org/10.1093/oxfordjournals.molbev.a003917
Abbott CL, Double MC, Trueman JW, Robinson A, Cockburn A (2005) An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses. Mol Ecol 14:3605–3613. https://doi.org/10.1111/j.1365-294X.2005.02672.x
Singh TR, Shneor O, Huchon D (2008) Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes. Mol Biol Evol 25:475–477. https://doi.org/10.1093/molbev/msn003
Acknowledgements
The first author is thankful to the Kerala State Council for Science Technology and Environment (KSCSTE), Government of Kerala for the support in the form of a research fellowship. Karippadakam Bhavana was supported by the UGC (365844) through Ph.D fellowship. The authors are grateful to the anonymous reviewers for their valuable comments and suggestions which improved the manuscript. The authors are also grateful to Dr. Jacob Alexander, Veterinary Surgeon, Zoological Park, Trivandrum, Kerala.
Funding
The study was partially supported by the Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India, New Delhi (SR/S0/AS-84/2012).
Author information
Authors and Affiliations
Contributions
MN conceived the study. ST performed the experiments. HSS, ST, RK, KB and MN performed the analyses. MN, HSS, SG and KB wrote the manuscript. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This study does not require ethical approval as the tissue sample used was collected from deceased specimen.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Thomas, S., Singha, H.S., Kamalakkannan, R. et al. Analysis of the mitochondrial genome of the Indian darter, Anhinga melanogaster, suggests a species status taxonomic rank. Mol Biol Rep 48, 7343–7350 (2021). https://doi.org/10.1007/s11033-021-06737-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-021-06737-8