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      Evolutionary profile of the family Calliphoridae, with notes on the origin of myiasis

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          Abstract

          The family Calliphoridae is a group of heterogenous calyptrate flies with a worldwide distribution including species of ecological, veterinary, medical, and forensic importance. Notorious for their parasitic habits, the larvae of many blowflies are characterised – like some other dipteran larvae – by their ability to develop in animal flesh. When parasitism affects a living host, it is termed “myiasis”. This has led the Calliphoridae to be considered as a pivotal family in its relationship with a man. Nevertheless, even after more than 50 years of research, the phylogenetic relationships among calliphorid subfamilies together with the evolutionary origin of myiasis remain unclear. In order to elucidate these problems, we constructed three phylogenetic trees by using nucleotide sequence data from cytochrome oxidase subunit one ( COI), representing a mitochondrial conservative gene, and nuclear 28S subunit of ribosomal RNA gene ( 28S rRNA) in order to interpret the evolutionary profile of myiasis in the family Calliphoridae. The sequenced data represented species associated with ectoparasitic life-styles, either saprophagy or facultative and obligate parasitism. A total number of 50 accessions were collected for 28S rRNA, 56 for COI, and 38 for combined sequences phylogeny. Molecular Evolutionary Genetics Analysis (MEGA) software was used to align 2197 nucleotide positions of 28S rRNA and 1500 nucleotide positions of COI with a gap opening penalties and gap extension penalties equalling 20 and 0.1 respectively. The results reveal the non-monophyly of the family Calliphoridae despite the stable monophyletic status of the Chrysomyinae, Luciliinae, and Auchmeromyiinae. Also, our findings recommend ranking the Toxotarsinae as a separate family. Furthermore, comparative analysis of the phylogenetic trees shows that the habit of obligatory myiasis originated independently more than five times. This strengthens our hypothesis that the origin of eating fresh meat is a case of convergent evolution that has taken place after speciation events millions of years ago. Finally, estimating the divergence dates between lineages from molecular sequences provides a better chance of understanding their evolutionary biology.

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          Most cited references40

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          MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

          We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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            CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.

            The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
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              Estimation of evolutionary distance between nucleotide sequences.

              F Tajima, M Nei (1984)
              A mathematical formula for estimating the average number of nucleotide substitutions per site (delta) between two homologous DNA sequences is developed by taking into account unequal rates of substitution among different nucleotide pairs. Although this formula is obtained for the equal-input model of nucleotide substitution, computer simulations have shown that it gives a reasonably good estimate for a wide range of nucleotide substitution patterns as long as delta is equal to or smaller than 1. Furthermore, the frequency of cases to which the formula is inapplicable is much lower than that for other similar methods recently proposed. This point is illustrated using insulin genes. A statistical method for estimating the number of nucleotide changes due to deletion and insertion is also developed. Application of this method to globin gene data indicates that the number of nucleotide changes per site increases with evolutionary time but the pattern of the increase is quite irregular.
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                Author and article information

                Contributors
                Journal
                Saudi J Biol Sci
                Saudi J Biol Sci
                Saudi Journal of Biological Sciences
                Elsevier
                1319-562X
                2213-7106
                28 January 2021
                April 2021
                28 January 2021
                : 28
                : 4
                : 2056-2066
                Affiliations
                [a ]Department of Entomology, Faculty of Science, Ain Shams University, Abbassia, Cairo, Egypt
                [b ]Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
                [c ]Department of Oral & Maxillofacial Surgery, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11545, Saudi Arabia
                [d ]Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
                Author notes
                [* ]Corresponding author. iobek@ 123456sci.asu.edu.eg
                Article
                S1319-562X(21)00032-2
                10.1016/j.sjbs.2021.01.032
                8071908
                33911921
                4e956399-0872-40a5-98c0-03b2ad9af27b
                Crown Copyright © 2021 Published by Elsevier B.V. on behalf of King Saud University.

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 27 December 2020
                : 10 January 2021
                : 14 January 2021
                Categories
                Original Article

                blowflies,conservative genes,evolution,data science,phylogeny

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