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Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.<\/jats:p>","DOI":"10.1093\/gbe\/evz209","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T04:05:29Z","timestamp":1569902729000},"page":"2824-2849","source":"Crossref","is-referenced-by-count":39,"title":["Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications"],"prefix":"10.1093","volume":"11","author":[{"given":"Pawe\u0142","family":"Mackiewicz","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroc\u0142aw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam Dawid","family":"Urant\u00f3wka","sequence":"additional","affiliation":[{"name":"Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandra","family":"Kroczak","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroc\u0142aw, Poland"},{"name":"Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorota","family":"Mackiewicz","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroc\u0142aw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,3]]},"reference":[{"issue":"11","key":"2019101610590215700_evz209-B1","doi-asserted-by":"crossref","first-page":"3605","DOI":"10.1111\/j.1365-294X.2005.02672.x","article-title":"An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in 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