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Substitution Rate Estimation of Molecular Markers to Evaluate Evolutionary Aspects in Ladybird Beetles


Affiliations
1 Ladybird Research Laboratory, Department of Zoology, University of Lucknow, Lucknow 226 007, India
 

In this study, we examined the ribosomal DNA internal transcribed spacers and mtDNA markers for their use in the prospecting of 480 ladybird species belonging to 14 tribes to assess the evolutionary topology and substitution rates. Substitution patterns of the respective markers were estimated using a cascade of algorithms such as pairwise sequence comparisons, maximum likelihood estimates of the substitution matrix, transitions/transversions (ti/tv) and gamma parameters with a suitable substitution model. Maximum likelihood (ML) estimates showed that COI (R = 1.16) and COII (R = 1.36) were more biased towards transitions. COI has a higher ti/tv ratio indicating more substitutions and less divergence among the species in the phylogenetic tree, though it had moderate bootstrap support. ML and Bayesian analysis were used to construct the morphology character matrix and molecular datasets in order to establish the evolutionary relationship. All the characters of male and female genitalia supported mophyletic topology. The phylogenetic results of molecular datasets suggest that most of the taxa significantly support monophyly. Phylogenetic analysis depict COI consists of more substitution as it shows less divergence among species.

Keywords

Evolutionary Topology, Ladybirds, Molecular Markers, Phylogenetic Analysis, Substitution Rates.
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  • Vandenberg, N. J., 93. Coccinellidae Latreille 1807, American Beetles (eds Arnett Jr, R. H. and Thomas, M. C.), CRC Press, 2002, vol. 2, pp. 371–389.

  • Seago, A. E., Giorgi, J. A., Li, J. and Slipinski, A., Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data. Mol. Phylogenet. Evol., 2011, 60(1), 137–151.

  • Poorani, J., Coccinellidae of the Indian subcontinent. In Indian Insects, CRC Press, 2019, pp. 223–246.

  • Szawaryn, K., Bocak, L., Ślipiński, A., Escalona, H. E. and Tomaszewska, W., Phylogeny and evolution of phytophagous ladybird beetles (Coleoptera: Coccinellidae: epilachnini), with recognition of new genera. Syst. Entomol., 2015, 40(3), 547–569.

  • Hodek, I., Honek, A. and Van Emden, H. F. (eds), Ecology and Behaviour of the Ladybird Beetles (Coccinellidae), John Wiley & Sons, 2012.

  • Giorgi, J. A. et al., The evolution of food preferences in Coccinellidae. Biol. Control, 2009, 51(2), 215–231.

  • Magro, A., Lecompte, E., Magne, F., Hemptinne, J. L. and Crouau-Roy, B., Phylogeny of ladybirds (Coleoptera: Coccinellidae): are the subfamilies monophyletic? Mol. Phylogenet. Evol., 2010, 54(3), 833–848.

  • Atif, J. Y., El-Husseini, M. M., Al-Shemi, H. A. and Ahmed, S. S., Molecular identification of five Egyptian lady bird beetles based on 28S rDNA (Coleoptera: Coccinellidae). Egypt. J. Biol. Pest Control, 2016, 26(1).

  • Escalona, H. E. et al., Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini). BMC Evol. Biol., 2017, 17(1), 1–11.

  • Robertson, J. A. et al., Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia). Syst. Entomol., 2015, 40(4), 745–778.

  • De Mandal, S., Chhakchhuak, L., Gurusubramanian, G. and Kumar, N. S., Mitochondrial markers for identification and phylogenetic studies in insects – a review. DNA Barcodes, 2014, 2(1), 1–9.

  • Mahmoud, A. G. Y. and Zaher, E. H. F., Why nuclear ribosomal internal transcribed spacer (ITS) has been selected as the DNA barcode for fungi. Adv. Genet. Eng., 2015, 4(119), 2169–0111.

  • Jay, P., Chouteau, M., Whibley, A., Bastide, H., Parrinello, H., Llaurens, V. and Joron, M., Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nature Genet., 2021, 53(3), 288–293.

  • Von der Schulenburg, J. H. G., Hancock, J. M., Pagnamenta, A., Sloggett, J. J., Majerus, M. E. and Hurst, G. D., Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae). Mol. Biol. Evol., 2001, 18(4), 648–660.

  • Zhao, Y., Tsang, C. C., Xiao, M., Cheng, J., Xu, Y., Lau, S. K. and Woo, P. C., Intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology. Int. J. Mol. Sci., 2015, 16(10), 25067–25079.

  • Badotti, F. et al., Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (fungi). BMC Microbiol., 2017, 17(1), 1–12.

  • Yang, R. H., Su, J. H., Shang, J. J., Wu, Y. Y., Li, Y., Bao, D. P. and Yao, Y. J., Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing. PLoS ONE, 2018, 13(10), e0206428.

  • Edger, P. P. et al., Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards). PLoS ONE, 2014, 9(7), e101341.

  • Nolan, M. J. and Cribb, T. H., The use and implications of ribosomal DNA sequencing for the discrimination of digenean species. Adv. Parasitol., 2005, 60, 101–163.

  • Schlötterer, C., Hauser, M. T., von Haeseler, A. and Tautz, D., Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol. Biol. Evol., 1994, 11(3), 513–522.

  • Song, N., Li, X., Yin, X., Li, X. and Xi, Y., The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny. Int. J. Biol. Macromol., 2020, 147, 1193–1203.

  • Cameron, S. L., Insect mitochondrial genomics: implications for evolution and phylogeny. Annu. Rev. Entomol., 2014, 59, 95–117.

  • Aruggoda, A. G. B., Shunxiang, R. and Baoli, Q., Molecular phylogeny of ladybird beetles (Coccinellidae: Coleoptera) inferred from mitochondrial 16S rDNA sequences. Trop. Agric. Res., 2010, 21(2), 209–217.

  • Correa, C. C. and Ballard, J. W. O., Wolbachia associations with insects: winning or losing against a master manipulator. Front. Ecol. Evol., 2016, 3, 153.

  • Sato, M. and Sato, K., Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA. Biochim. Biophys. Acta – Mol. Cell Res., 2013, 1833(8), 1979–1984.

  • Poolprasert, P., Senarat, S., Nak-eiam, S. and Likhitrakarn, N., Molecular taxonomic identification of predatory ladybird beetles inferred from COI sequences (Coleoptera: Coccinellidae). Malaysian J. Appl. Sci., 2019, 4(2), 10–18.

  • Ghosh, S., Behere, G. T. and Agarwala, B. K., Molecular characterization of ladybird predators (Coleoptera: Coccinellidae) of aphid pests (Homoptera: Aphididae) in North East India. Curr. Sci., 2017, 113, 1755–1759.

  • Lin, C. P. and Danforth, B. N., How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol. Phylogenet. Evol., 2004, 30(3), 686–702.

  • Kaltenpoth, M., Corneli, P. S., Dunn, D. M., Weiss, R. B., Strohm, E. and Seger, J., Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps. PLoS ONE, 2012, 7(3), e32826.

  • Chang, H. et al., Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types. Mol. Phylogenet. Evol., 2020, 145, 106734.

  • Li, T., Hua, J., Wright, A. M., Cui, Y., Xie, Q., Bu, W. and Hillis, D. M., Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evol. Biol., 2014, 14(1), 99.

  • Qu, X. J., Jin, J. J., Chaw, S. M., Li, D. Z. and Yi, T. S., Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae). Sci. Rep., 2017, 7(1), 1–11.

  • Hung, J. H. and Weng, Z., Sequence alignment and homology search with BLAST and ClustalW. Cold Spring Harb. Protoc., 2016, 11, pdb-prot093088.

  • Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K., MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 2018, 35, 1547–1549.

  • Xu, X. and Reid, N., On the robustness of maximum composite likelihood estimate. J. Stat. Plan. Inference, 2011, 141(9), 3047–3054.

  • Tamura, K. and Kumar, S., Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol., 2002, 19(10), 1727–1736.

  • Myung, I. J., Tutorial on maximum likelihood estimation. J. Math. Psychol., 2003, 47(1), 90–100.

  • Watanabe, S., A widely applicable Bayesian information criterion. J. Mach. Learn. Res., 2013, 14, 867–897.

  • Ronquist, F. et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol., 2012, 61(3), 539–542.

  • Gascuel, O., BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol., 1997, 14(7), 685–695.

  • Maddison, W. P. and Maddison, D. R., Mesquite: a modular system for evolutionary analysis. Version 3.70. 2021; http://www.mesquiteproject.org

  • Brennan, P. L. and Orbach, D. N., Copulatory behavior and its relationship to genital morphology. In Advance Study Behaviour, Academic Press, 2020, vol. 52, pp. 65–122.

  • Verma, C., Mishra, G. and Omkar, Widespread inspection and comparative analysis of ITS secondary structure conservation and covariation of Coccinellidae. Int. J. Trop. Insect Sci., 2020, 40(3), 587–597.

  • Tomaszewska, W. et al., Phylogeny of true ladybird beetles (Coccinellidae: Coccinellini) reveals pervasive convergent evolution and a rapid Cenozoic radiation. Syst. Entomol., 2021, 46(3), 611–631.

  • Stoltzfus, A. and Norris, R. W., On the causes of evolutionary transition: transversion bias. Mol. Biol. Evol., 2016, 33(3), 595–602.

  • Homem, R. A., Buttery, B., Richardson, E., Tan, Y., Field, L. M., Williamson, M. S. and Emyr Davies, T. G., Evolutionary trade-offs of insecticide resistance – the fitness costs associated with target-site mutations in the nAChR of Drosophila melanogaster. Mol. Ecol., 2020, 29(14), 2661–2675.

  • Sahu, R., Biswal, D. K., Roy, B. and Tandon, V., Molecular characterization of Opisthorchis noverca (Digenea: Opisthorchiidae) based on nuclear ribosomal ITS2 and mitochondrial COI genes. J. Helminthol., 2016, 90(5), 607–614.

  • Greczek-Stachura, M., Potekhin, A., Przyboś, E., Rautian, M., Skoblo, I. and Tarcz, S., Identification of Paramecium bursaria Syngens through molecular markers – comparative analysis of three loci in the nuclear and mitochondrial DNA. Protist, 2012, 163(5), 671–685.

  • Ghada, B., Ahmed, B. A., Messaoud, M. and Amel, S. H., Genetic diversity and molecular evolution of the internal transcribed spacer (ITSs) of nuclear ribosomal DNA in the Tunisian fig cultivars (Ficus carica L.; Moracea). Biochem. Syst. Ecol., 2013, 48, 20–33.

  • Martyn, I. and Steel, M., The impact and interplay of long and short branches on phylogenetic information content. J. Theor. Biol., 2012, 314, 157–163.

  • James, J. E., Piganeau, G. and Eyre-Walker, A., The rate of adaptive evolution in animal mitochondria. Mol. Ecol., 2016, 25(1), 67–78.

  • Duchêne, S., Ho, S. Y. and Holmes, E. C., Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models. BMC Evol. Biol., 2015, 15(1), 36.

  • Yan, Z., Ye, G. and Werren, J. H., Evolutionary rate correlation between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins in insects. Mol. Biol. Evol., 2019, 36(5), 1022–1036.

  • Bromham, L., Substitution rate analysis and molecular evolution. Phylogenet. Genomic Era, 2020, 4.


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  • Substitution Rate Estimation of Molecular Markers to Evaluate Evolutionary Aspects in Ladybird Beetles

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Authors

Chandni Verma
Ladybird Research Laboratory, Department of Zoology, University of Lucknow, Lucknow 226 007, India
Geetanjali Mishra
Ladybird Research Laboratory, Department of Zoology, University of Lucknow, Lucknow 226 007, India
Omkar
Ladybird Research Laboratory, Department of Zoology, University of Lucknow, Lucknow 226 007, India

Abstract


In this study, we examined the ribosomal DNA internal transcribed spacers and mtDNA markers for their use in the prospecting of 480 ladybird species belonging to 14 tribes to assess the evolutionary topology and substitution rates. Substitution patterns of the respective markers were estimated using a cascade of algorithms such as pairwise sequence comparisons, maximum likelihood estimates of the substitution matrix, transitions/transversions (ti/tv) and gamma parameters with a suitable substitution model. Maximum likelihood (ML) estimates showed that COI (R = 1.16) and COII (R = 1.36) were more biased towards transitions. COI has a higher ti/tv ratio indicating more substitutions and less divergence among the species in the phylogenetic tree, though it had moderate bootstrap support. ML and Bayesian analysis were used to construct the morphology character matrix and molecular datasets in order to establish the evolutionary relationship. All the characters of male and female genitalia supported mophyletic topology. The phylogenetic results of molecular datasets suggest that most of the taxa significantly support monophyly. Phylogenetic analysis depict COI consists of more substitution as it shows less divergence among species.

Keywords


Evolutionary Topology, Ladybirds, Molecular Markers, Phylogenetic Analysis, Substitution Rates.

References





DOI: https://doi.org/10.18520/cs%2Fv124%2Fi4%2F491-499