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Background   Habronattus  is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict.    Results  To infer  Habronattus  phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34  Habronattus  species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of  H. icenoglei ,  H. cambridgei, H. oregonensis,  and  Pellenes canadensis . Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the  americanus  and the  coecatus  groups, the relationship between the  altanus, decorus, banksi , and  americanus  group, and between  H. clypeatus  and the  coecatus  group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the  americanus  group (679 loci) and the VCCR clade ( viridipes/clypeatus/coecatus/roberti  groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson’s D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between  americanus  group species ,  between  H. roberti  and the  clypeatus  group, and between the  clypeatus  and  coecatus  groups.    Conclusions  Our results indicate that the phylogenetic history of  Habronattus  is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1137-x) contains supplementary material, which is available to authorized users.

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)