Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

“…Our methodology allowed us to infer the phylogeny of 41 tephritid specimens belonging to five genera and seven Anastrepha species groups based on more than 2000 loci. In general, phylogenetic inferences agree with the current taxonomy of these taxa (Norrbom et al, 1999;Zucchi, 2000b), as species groups are recovered as monophyletic, and samples from the same species are allocated to the same lineages, except for the A. fraterculus complex, which was confirmed to be polyphyletic (Congrains et al, 2021;Mengual et al, 2017;Scally et al, 2016;Smith-Caldas et al, 2001). Furthermore, our results corroborate that the A. fraterculus complex, A. obliqua, A. turpiniae, and A. suspensa have diverged under the presence of gene flow, which has previously been suggested for those and other species of the fraterculus group (Congrains et al, 2021;Díaz et al, 2018;Scally et al, 2016).…”

“…In general, phylogenetic inferences agree with the current taxonomy of these taxa (Norrbom et al, 1999;Zucchi, 2000b), as species groups are recovered as monophyletic, and samples from the same species are allocated to the same lineages, except for the A. fraterculus complex, which was confirmed to be polyphyletic (Congrains et al, 2021;Mengual et al, 2017;Scally et al, 2016;Smith-Caldas et al, 2001). Furthermore, our results corroborate that the A. fraterculus complex, A. obliqua, A. turpiniae, and A. suspensa have diverged under the presence of gene flow, which has previously been suggested for those and other species of the fraterculus group (Congrains et al, 2021;Díaz et al, 2018;Scally et al, 2016). Despite this complex evolutionary scenario, we showed that sampling as few as 30 genes can provide resolution to most clades and sampling up to 80 or more genes may be required to have enough phylogenetic information to confidently reconstruct the phylogeny of this troublesome group.…”

“…If introgression is the main source of these incongruences, we would expect to have recovered those clades with reticulation in the networks. As the networks did not show reticulations directly associated with Clade 2 and Clade 5, we suggest that the informative set of genes may be recalcitrant to the impacts of gene flow (Congrains et al, 2021), even for A. fraterculus lineages.…”

“…The existence of multiple cryptic lineages within the A. fraterculus complex is supported by evidence from various sources, including morphometric analyses (Hernández-Ortiz et al, 2012. More recently, there has been indication that some of that divergence is associated with variation in the ITS1 region (Prezotto et al, 2019;Sutton et al, 2015), which makes it relevant for us to try to use that information to associate the previously recognized entities within the A. fraterculus complex with our phylogenomic assess- fraterculus (Table 2; Congrains et al, 2021;Goday et al, 2006;Hernández-Ortiz et al, 2012;Selivon et al, 2004Selivon et al, , 2005Sutton et al, 2015). Two A. fraterculus CVI specimens were sampled from localities close to where Anastrepha sp.…”

“…Several multispecies coalescent methods can accommodate gene tree heterogeneity by treating it as caused by ILS but may be inconsistent under the presence of gene flow between species (Solís- Lemus et al, 2016). Introgression among fraterculus group lineages has been previously reported (Congrains et al, 2021;Díaz et al, 2018), but these studies lacked the wider array of lineages from the A. fraterculus complex that we included in this study. The…”