Molecular phylogenies of foraminifera are commonly inferred from the small subunit rRNA (SSU) genes, which can easily be obtained from single cells isolated from environmental samples. The SSU phylogenies, however, are often biased by heterogeneity of substitution rates, and their resolution of higher level relationships is often very low. The sequences of protein-coding genes provide an important alternative source of phylogenetic information, yet their availability from foraminifera has been limited until now. Here, we report the first extensive protein sequence data for foraminifera, which comprises 90 actin sequences for 27 species representing five major foraminiferan groups. Our analysis enables grouping foraminiferan actins into two main paralogs, ACT1 (actin type 1) and ACT2 (actin type 2), and several actin-deviating proteins. Phylogenetic analyses of ACT1 and ACT2 confirm the general structure of foraminiferan phylogenies inferred from SSU rDNA sequences. In particular, actin phylogenies support (1) the paraphyly of monothalamous foraminifera, including the allogromiids, astrorhizids and athalamids; (2) the independent divergence of miliolids and their close relationship to Miliammina; (3) the monophyly of rotalids; and (4) the rotaliid ancestry of globigerinids. Some foraminiferan taxa can be distinguished in actin sequences by the presence of group-specific introns (rotaliids, allogromiids) or absence of any introns (soritids ACT1).

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