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Phylogenetic Confli...
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- Article/chapterEnglish2023
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LIBRIS-ID:oai:gup.ub.gu.se/334769
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https://gup.ub.gu.se/publication/334769URI
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https://doi.org/10.1093/sysbio/syad078DOI
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
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Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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She, Huishang
(author)
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Wang, Shangyu
(author)
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Wang, Haitao
(author)
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Li, Shi
(author)
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Cheng, Yalin
(author)
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Song, Gang
(author)
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Jia, Chenxi
(author)
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Qu, Yanhua
(author)
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Rheindt, Frank E.
(author)
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Olsson, Urban,1954Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xolsur
(author)
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Alstroem, Per
(author)
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Lei, Fumin
(author)
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Göteborgs universitetInstitutionen för biologi och miljövetenskap
(creator_code:org_t)
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In:SYSTEMATIC BIOLOGY1063-51571076-836X
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Zhang, Dezhi
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She, Huishang
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Wang, Shangyu
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Wang, Haitao
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Li, Shi
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Cheng, Yalin
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Song, Gang
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Jia, Chenxi
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Qu, Yanhua
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Rheindt, Frank E ...
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Olsson, Urban, 1 ...
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Alstroem, Per
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Lei, Fumin
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
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SYSTEMATIC BIOLO ...
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University of Gothenburg