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. 2021 Jun 8;22:422. doi: 10.1186/s12864-021-07722-y

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Sibling species differentiation. a t-SNE plot highlighting genes that show two criteria: Species F_ST higher than General F_ST and Species F_ST values higher than 0.5 (red). These genes are largely located either on the centromeric half of the X chromosome or close to the 3R centromere. In black, gene Vgsc (AGAP004707). b Enlargement of the ‘speciation cluster’ showing neighboring genes (AGAP001073, AGAP001082, AGAP001083, AGAP001084) of the main diagnostic markers of A. gambiae and A. coluzzii: IGS, SINE200 and CYP (in blue). c Schematic representation of gene starting point for every gene selected in a; shaded area corresponds to previously described islands of speciation. d Table containing the distribution of genes through chromosome arms in the ‘speciation cluster’. e Scatter plot of the same 11,318 genes of A. gambiae genome using only An. gambiae s.s. samples, showing loss of a defined ‘speciation cluster’