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

Abstract

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

Fig. 1. Phylogeny and ancestral character state reconstruction of the nitrogen-fixing clade (NFC) in context within rosids.

NFC orders and legume subfamilies are indicated by colored bars; non-NFC clades are reduced in size (unlabeled section). Branches are colored by the state estimated at their tipward node, but to focus on the history of RNS-gain, all three hidden states of RNS-absent are colored blue. For each of 16 hypothesized independent gains, an image of a single representative taxon is indicated at its approximate phylogenetic position, except in the very species-rich clades where multiple representatives sharing a border color represent a single origin of RNS. Clockwise beginning at the top right in Papilionoideae, the pictured representatives are: (1) Astragalus, (2) Medicago, (3) Phaseolus, (4) Indigofera, (5) Lupinus, (6) Swartzia, (7) Mimosa, (8) Dimorphandra, (9) Moldenhawera, (10) Chamaecrista, (11) Melanoxylum, (12) Alnus, (13) Casuarina, (14) Myrica, (15) Ceanothus, (16) Trevoa, (17) Elaeagnus, (18) Dryas, and (19) Datisca. Image credits: (1) Astragalus – Photo taken from Wikimedia user Kaldari from Wikipedia.org https://en.wikipedia.org/wiki/Astragalus_nuttallianus#/media/File:Fabaceae_flowers_Texas.jpg 2009. Public Domain. (2) Medicago – Photo taken from Wikimedia user Ninjatacoshell from Wikipedia.org https://en.wikipedia.org/wiki/Medicago_truncatula#/media/File:Medicago_truncatula_A17_branch.JPG 2009. CC BY-SA 3.0. (3) Lotus – Photo taken from Wikimedia user Hans Hillewaert from Wikipedia.org https://commons.wikimedia.org/wiki/Lotus_cytisoides#/media/File:Lotus_cytisoides.jpg 2008. CC BY-SA 3.0. (4) Indigofera – Photo taken from Wikimedia user Kurt Stüber from Wikipedia.org https://en.wikipedia.org/wiki/Indigofera_tinctoria#/media/File:Indigofera_tinctoria1.jpg 2004. CC BY-SA 3.0. (5) Lupinus – Photo taken from Wikimedia user Banana patrol from Wikipedia.org https://commons.wikimedia.org/wiki/File:Lupinus_polyphyllus.JPG 2005. CC BY-SA 3.0. (6) Swartzia - Photo taken from Wikimedia user Vojtěch Zavadil from Wikipedia.org https://commons.wikimedia.org/wiki/File:13010-Swartzia_picta-Caura.JPG 2007. CC BY-SA 3.0. (7) Mimosa - Photo taken from Wikimedia user Don McCulley from Wikipedia.org https://commons.wikimedia.org/wiki/Category:Mimosa_pudica_(flowers)#/media/File:Mimosa_pudica_IMG_0230.jpg 2018. CC BY-SA 4.0. (8) Dimorphandra - Photo taken from Wikimedia user Denis A. C. Conrado from Wikipedia.org. https://commons.wikimedia.org/wiki/File:Favadanta03.jpg 2007. Use permitted by copyright holder. (9) Moldenhawera - Permission by Domingos Cardoso. (10) Chamaecrista - Photo taken from Wikimedia user Fritz Flohr Reynolds from Wikipedia.org https://commons.wikimedia.org/wiki/Category:Chamaecrista_fasciculata#/media/File:Chamaecrista_fasciculata_-_Partridge_Pea.jpg 2013. CC BY-SA 3.0. (11) Melanoxylum - Permission by Domingos Cardoso. (12) Alnus - Photo taken from Wikimedia user Noël Zia Lee from Wikipedia.org https://commons.wikimedia.org/wiki/Alnus#/media/File:Red_Alder_Female_Catkins_in_Autumn.jpg 2007. CC BY 2.0. (13) Casuarina - Photo taken from Wikimedia user Sam Fraser-Smith from Wikipedia.org https://commons.wikimedia.org/wiki/File:Casuarina_equisetifolia_L._-_Australian_pine,_beach_sheoak,_common_ironwood_(3771046132).jpg 2009. CC BY 2.0. (14) Myrica - Photo taken from Wikimedia user Ettrig from Wikipedia.org https://commons.wikimedia.org/wiki/File:Myrica_faya.jpg 2006. Public Domain. (15) Ceanothus - Photo taken from Wikimedia user Stan Shebs from Wikipedia.org https://en.wikipedia.org/wiki/Ceanothus_pauciflorus#/media/File:Ceanothus_greggii_4.jpg 2006. CC BY-SA 3.0. (16) Trevoa - Photo taken from Wikimedia user Dick Culbert from Wikipedia.org https://commons.wikimedia.org/wiki/Category:Trevoa_quinquenervia#/media/File:Trevoa_quinquenervia_of_the_Rhamnaceae_(8405983258).jpg 2006. CC BY 2.0 (17) Elaeagnus - Photo taken from Wikimedia user KENPEI from Wikipedia.org https://en.m.wikipedia.org/wiki/File:Elaeagnus_umbellata1.jpg 2008. CC BY-SA 2.1 (18) Dryas - Photo taken from Wikimedia user Kim Hansen from Wikipedia.org https://commons.wikimedia.org/wiki/File:Dryas_integrifolia_upernavik_2007_06_28_1.jpg 2007. CC BY-SA 3.0 (19) Datisca - Photo taken from Wikimedia user H. Zell from Wikipedia.orghttps://commons.wikimedia.org/wiki/Category:Datisca_cannabina#/media/File:Datisca_cannabina_002.JPG 2009. CC BY 3.0 Links to licenses for reuse restrictions: CC BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/ CC BY 3.0: https://creativecommons.org/licenses/by/3.0/deed.en CC BY-SA 2.1: https://creativecommons.org/licenses/by-sa/2.1/ca/deed.en CC BY 2.0: https://creativecommons.org/licenses/by/2.0/deed.en CC BY-SA 3.0: https://creativecommons.org/licenses/by-sa/3.0/deed.en Public Domain: https://wiki.creativecommons.org/wiki/public_domain.

Fig. 2. Model of a two-step pathway to the gain of nodulation.

A simplified depiction of the rate transition network inferred by the best hidden rates model to highlight pathways to gaining RNS (“RNS-present”) within the NFC. The three RNS-present hidden-states are combined into a single RNS-present (any rate category) state. Transition rates from each of the three inferred RNS-absent hidden states are drawn with width relative to the speed of the transition. Transition arrows are colored by the state from which they originate to correspond with how inferred states are colored on the phylogeny in Fig. 1. Two types of gears in the figure (orange and red) represent two levels of homology as predicted by a two-step pathway, only one of which occurs in the precursor. Subsequent changes in gear shape represent pseudogenization and other non-functionalization processes in nodulation pathways. An illustration of the full transition rate matrix is shown in Supplementary Fig. 13.