Supermatrix analyses and molecular clock rooting of Fabales: Exploring the effects of outgroup choice and long branch attraction on topology

Abstract

Fabales is a cosmopolitan angiosperm order that consists of four families: Leguminosae (Fabaceae), Polygalaceae, Surianaceae, and Quillajaceae. Despite the great interest in this group, a convincing phylogeny of the order is still not available. Therefore, the aim of this study was to explicitly test for possible long branch attraction (LBA) problems within Fabales for the first time, and determine whether low tree stemminess and unequal branch lengths could worsen this problem. Supermatrix analysis of Fabales was carried out using previously published plastid matK, trnL, rbcL, and newly sequenced nuclear sqd1 regions for 678 taxa in total, including 43 outgroup taxa from families of Fabidae. We employed additional analyses, such as simulations, network analyses, sampling different outgroup taxa (random or real), removing fast evolving sites and fast evolving taxa, and molecular clock rooting, to identify both LBA and (or) rooting problems. These analyses clearly show that the Fabales phylogeny has been influenced by the sampling of outgroup taxa, but not LBA. However, network analyses show that even though it is weak, there is a consistent phylogenetic signal among the rapidly radiated Fabales families, which can be traced by further analyses. While, molecular clock rooting analysis yielded a (Leguminosae(Polygalaceae(Surianaceae+Quillajaceae))) topology with strong support for the first time here, supermatrix analyses yielded a ((Leguminosae+Polygalaceae)(Surianaceae+Quillajaceae)) with low-moderate support.

Reconstructing an historical pollination syndrome: keel flowers

“…The divergence-time analysis was congruent with previous studies (e.g., [ 12 , 39 ]), with short internal branches of Fabales reflecting the rapid radiation already highlighted for this clade [ 12 , 48 , 49 ]. The divergence-time analysis also showed that keel flowers in crown Papilionoideae 67.19 Ma (95% HPD 62.5–64.9) evolved before the origin of Polygalaceae (63.59 Ma, 95% HPD 62.7–58.2 Ma) and tribe Polygaleae (45.16, 95% HPD 44.7–38.8 Ma), even if we accept Xanthophyllum as polymorphic in terms of the presence or absence of keel-flowers [ 50 ].…”

“…Similarly, the evolutionary origin of the six subfamilies of Fabaceae has been reported as near simultaneous [ 81 ]. While the current study exceeds the taxon sampling of Bello et al [ 12 , 17 ], Aygoren Uluer et al [ 49 ] and Koenen et al [ 81 , 82 ], it is the same as Aygoren Uluer et al [ 48 ]; however, none of these studies were able to support a robust topology for the order. Furthermore, Koenen et al’s [ 81 ] recently published phylogeny of the early evolving Leguminosae based on 1103 nuclear orthologues included only two Polygalaceae and one Surianaceae taxa, and therefore, it would not be possible to explore our molecular dating and ancestral reconstructions on their trees.…”

“…Whilst recent studies have employed considerable more sequence data (e.g., [ 80 – 82 ]), these data are not presently available across the Fabales. The monophylly of Fabales has been strongly supported; yet, both the fossil record and molecular studies (e.g., [ 12 , 17 , 48 , 49 ]) suggest a rapid radiation for the order, which causes unstable phylogenetic relationships among the four families, namely, change in the topology and the root of the order by the choice of genes, outgroups and phylogenetic methods. Similarly, the evolutionary origin of the six subfamilies of Fabaceae has been reported as near simultaneous [ 81 ].…”

Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

“…However, current considerations of RNS evolution still rely on phylogenies with limited taxon and trait sampling 13 . While fully resolved phylogenies remain elusive for many deep branches in the plant tree of life such as those in the NFC 27 , 28 , results based on large, multi-locus nuclear datasets offer clear advantages over those inferred from other types of data 29 . We construct such a phylogeny of the NFC based on ~13,000 species to ask whether RNS evolved once or many times and identify the origins of RNS within the NFC.…”

Toward New Generic Delimitations in Polygalaceae II: Senega

“…cons., together with Fabaceae Lindl. and two small families, Quillajaceae D. Don and Surianaceae Arn., belong to the order Fabales, with its monophyly demonstrated in several studies (Persson, 2001;Forest et al, 2007;Bello et al, 2012;APG IV, 2016;Uluer et al, 2020). Polygalaceae are divided into two subfamilies: Polygaloideae (comprising three tribes: Carpolobieae B. Eriksen, Diclidanthereae Reveal, and Polygaleae Fr.)…”