Hostname: page-component-586b7cd67f-l7hp2 Total loading time: 0 Render date: 2024-11-22T18:37:42.165Z Has data issue: false hasContentIssue false

Correlated evolution of seed mass and genome size varies among life forms in flowering plants

Published online by Cambridge University Press:  13 May 2022

Angelino Carta*
Affiliation:
Department of Biology, Botany Unit, University of Pisa, Pisa, Italy
Efisio Mattana
Affiliation:
Royal Botanic Gardens, Kew, Wakehurst, West Sussex, UK
John Dickie
Affiliation:
Royal Botanic Gardens, Kew, Wakehurst, West Sussex, UK
Filip Vandelook
Affiliation:
Meise Botanic Garden, Meise, Belgium
*
*Correspondence: Angelino Carta, E-mail: [email protected]
Rights & Permissions [Opens in a new window]

Abstract

Seeds show important variation as plant regenerative units among species, but their evolutionary co-variations with other plant characteristics are still poorly understood. Whilst a positive association of seed mass with genome size (GS) and life forms has already been documented, a broad-scale quantification of their evolutionary correlation and adaptive selection has never been conducted. Here, we tested for correlated evolution of seed mass and GS towards distinct selective regimes related to life form in angiosperms. In particular, we tested the hypothesis that the selection toward lighter seeds and smaller genomes is stronger for annual plants, ensuring high regenerative potential. Using multivariate evolutionary models over a dataset containing 3242 species, we showed an overall positive correlated evolution of seed mass and GS deviating from a pure drift process. Instead, evolutionary changes in seed and genome sizes were driven by adaptive selection towards optimal values differing among life forms. Specifically, the evolutionary optima towards which the seed and genome sizes evolve show a covariation toward small values in annuals, intermediate values in perennial herbs and a trade-off between seed mass and GS in woody plants. Moreover, the evolutionary correlation between seed mass and GS is strongest in annuals as an adaption to complete their life cycle in a short time window, when environmental conditions are favourable for regeneration and development to maturity. The asymmetry in the correlated evolution acting on seed and genome sizes due to life form could explain how life-history traits interplay with functional traits and how plants have evolved diverse successful life-history strategies.

Type
Research Paper
Creative Commons
Creative Common License - CCCreative Common License - BYCreative Common License - NCCreative Common License - SA
This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike licence (https://creativecommons.org/licenses/by-nc-sa/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the same Creative Commons licence is included and the original work is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use.
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press

Introduction

One of the main reasons for the evolutionary success of flowering plants is the vast diversity of their seed morphology and functions (Eriksson et al., Reference Eriksson, Friis and Löfgren2000; Linkies et al., Reference Linkies, Graeber, Knight and Leubner-Metzger2010; Baskin and Baskin, Reference Baskin and Baskin2014). This diversity in seed forms and functions is accompanied by a high variability in seed mass, a trait that is central to many features in plant ecology and evolution (Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005; Sims, Reference Sims2013; Igea et al., Reference Igea, Miller, Papadopulos and Tanentzap2017). Seed mass is indeed a trait associated with other vegetative, physiological and reproductive traits, linked to critical stages of a plant's life history, including seed/fruit production (Bolmgren and Eriksson, Reference Bolmgren and Eriksson2010), dispersal (Howe and Smallwood, Reference Howe and Smallwood1982; Chen et al., Reference Chen, Poschlod, Antonelli, Liu and Dickie2020), persistence (Thompson et al., Reference Thompson, Band and Hodgson1993; Long et al., Reference Long, Gorecki, Renton, Scott, Colville, Goggin and Finch-Savage2015; Gioria et al., Reference Gioria, Pyšek, Baskin and Carta2020), germination (Baskin and Baskin, Reference Baskin and Baskin2014) and seedling establishment (Moles and Westoby, Reference Moles and Westoby2004). Nevertheless, whilst seed mass has been found to be associated with other plant traits, the evolutionary co-variations of plant traits with seed mass are still not sufficiently understood. Thus, it is difficult to evaluate the consistency of functional traits’ relations and to disentangle them from traits’ evolutionary histories. For example, a generally positive correlation between seed mass and genome size (GS) across Spermatophytes has been shown, but this relationship is absent across Angiosperms (Beaulieu et al., Reference Beaulieu, Moles, Leitch, Bennett, Dickie and Knight2007), possibly because it is mediated by other ecological and functional constraints (Price, Reference Price1988; Veselý et al., Reference Veselý, Bureš, Šmarda and Pavlíček2012; Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021).

A dependence of seed mass on GS (i.e. the total amount of DNA in an unreplicated gametic nucleus, also known as a 1C value; Faizullah et al., Reference Faizullah, Morton, Hersch-Green, Walczyk, Leitch and Leitch2021) has long been sought (Beaulieu et al., Reference Beaulieu, Moles, Leitch, Bennett, Dickie and Knight2007). This dependence is likely driven by scaling relationships between GS and cell size and the number of cells in a tissue (Knight and Beaulieu, Reference Knight and Beaulieu2008). Indeed, whilst GS is highly variable across angiosperms (Pellicer et al., Reference Pellicer, Hidalgo, Dodsworth and Leitch2018; Pellicer and Leitch, Reference Pellicer and Leitch2020), there is strong evidence that it may act as a phenotypic trait, setting a lower limit on cell size, correlated with both cell division and tissue growth rate (Bennett, Reference Bennett1987; Knight and Beaulieu, Reference Knight and Beaulieu2008; Šímová and Herben, Reference Šímová and Herben2012). On the other hand, cell size and cell cycle times are correlated with a number of plant functional traits (including specific leaf area and xylem diameter; Faizullah et al., Reference Faizullah, Morton, Hersch-Green, Walczyk, Leitch and Leitch2021). In turn, natural selection acting on plant traits may also impact GS evolution, altogether leading to a correlation between GS and plant traits (Knight and Beaulieu, Reference Knight and Beaulieu2008). This may explain how GS, irrespectively of genic content, can impact species abundance, growth and fitness (Price, Reference Price1988; Carta and Peruzzi, Reference Carta and Peruzzi2016; Simonin and Roddy, Reference Simonin and Roddy2018; Faizullah et al., Reference Faizullah, Morton, Hersch-Green, Walczyk, Leitch and Leitch2021). Nevertheless, the relationship between GS and other plant traits decreases at higher ‘phenotypic scales’ (Knight and Beaulieu, Reference Knight and Beaulieu2008). Indeed, variation in seed mass is only marginally affected by changes in GS (Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021). The relation between GS and seed mass is a complex, non-linear association. Rather, GS is related to other life-history traits (including life forms; Stebbins, Reference Stebbins1938; Bennett, Reference Bennett1972; Bainard et al., Reference Bainard, Bainard, Henry, Fazekas and Newmaster2012; Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021) that are also shown to be important in the evolution of seed mass (Eriksson et al., Reference Eriksson, Friis and Löfgren2000; Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005).

GS and seed mass show significant phylogenetic clustering (Carta et al., Reference Carta, Bedini and Peruzzi2020; Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021) and a life-form-dependent distribution in GS and seed mass has been documented (Bennett, Reference Bennett1972; Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005; Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021). Accordingly, it is expected that annual herbaceous plants have lighter seeds and smaller genomes that enable rapid germination, exploitation of unpredictable habitats and completion of their life cycle before the end of the growing season (Stebbins, Reference Stebbins1938; Grant, Reference Grant1958; Harper, Reference Harper1977; Baskin and Baskin, Reference Baskin and Baskin2014). Woody angiosperms are not temporally limited like annuals, although some structural restrictions may exist regarding cell size, such as xylem diameter, with a negative effect on GS (Knight and Beaulieu, Reference Knight and Beaulieu2008). On the other hand, woody plants usually exhibit a higher investment in reserve and defence tissues in dispersal units (Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005). Moreover, woody plants take many years to reach reproductive maturity (Verdú, Reference Verdú2002), providing fewer opportunities to accumulate changes in GS (Beaulieu et al., Reference Beaulieu, Smith and Leitch2010). In short, woody and tall plants can have either large or small seeds, but smaller plants, be they annual or perennial, can only have relatively small seeds (Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005). Whilst perennial herbs usually have lighter seeds compared to woody plants, there is no obvious reason for them to be strongly limited in terms of GS (Leitch and Bennett, Reference Leitch, Bennett and Doležel2007). Rather, because of the positive relationship between generation time and GS, plants with larger genomes are usually perennials (Knight et al., Reference Knight, Molinari and Petrov2005) and are also thought to exhibit ecological constraints associated with larger GS (e.g. under-represented in extreme environments; Knight et al., Reference Knight, Molinari and Petrov2005). Altogether, it seems that differing GS and seed mass relations among life forms can be responsible for the absence of a direct relationship across angiosperms (Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021). However, to date, these hypotheses have not been supported by comparative studies of the correlated evolution of GS and seed mass using adaptive models.

Here, we used a macroevolutionary approach to formally test for correlated evolution of seed mass and GS towards distinct evolutionary optima according to different selective regimes related to life form in angiosperms. We applied two main classes of evolutionary models (Hansen, Reference Hansen1997): the Brownian motion (BM: stochastic evolution of continuously valued traits through time) and the Ornstein–Uhlenbeck (OU) process (adaptive evolution of traits toward optimal values). Specifically, by applying multivariate models of adaptive evolution (Clavel et al., Reference Clavel, Escarguel and Merceron2015) on data from 3242 species, we tested to what extent seed mass and GS are adaptations to plant life form. If seed mass and GS are highly adaptive traits, the OU models of trait evolution (modelling selection toward different optima according to different life forms) should outperform a pure drift trait evolution as described by BM models. Moreover, according to the expectations reported above, we should find both optimal seed mass and GS to be low in annuals, while a large evolutionary optimum in seed mass and a low optimum in GS are expected for woody plants. This prediction will be also evaluated by looking at the phenotypic evolutionary correlation between traits inferred from multivariate comparative models as this is also suggestive of different constraints acting within life forms.

Materials and methods

Data source

Seed mass data were extracted from the Seed Information Database (Royal Botanic Gardens Kew, 2022) and from TRY v5 (https://www.try-db.org; Kattge et al., Reference Kattge, Bönisch, Díaz, Lavorel, Prentice, Leadley and Cuntz2020). Seed mass data were combined with GS data (1C, prime estimates) taken from the Plant DNA C-values database (https://cvalues.science.kew.org/search/angiosperm, release 7.1, May 2020; Pellicer and Leitch, Reference Pellicer and Leitch2020). We also considered the monoploid GS (1Cx), calculated by dividing the 1C value by the ploidy level, allowing us to test for evolutionary covariation between both 1C DNA and 1Cx DNA content with seed mass. By repeating the analysis for both 1C and 1Cx, we could evaluate the effect of bulk genome content over the basal monoploid GS (the latter is much more associated with both meiosis and cell cycle duration; Beaulieu et al., Reference Beaulieu, Moles, Leitch, Bennett, Dickie and Knight2007). Moreover, as 1C evolution is largely affected by discrete transitions of ploidy level (e.g. polyploidization often followed by diploidization; Carta et al., Reference Carta, Bedini and Peruzzi2020), while the comparative adaptive models available model GS as a continuous quantitative process, it is important to use both 1C and 1Cx (the latter is much less influenced by discrete transitions; Beaulieu et al., Reference Beaulieu, Moles, Leitch, Bennett, Dickie and Knight2007) to test for GS-dependent relationships. We finally gathered 3242 and 2095 taxa, respectively, for 1C and 1Cx.

Mean seed mass and GS were calculated for each species, while within-species variation was not estimated separately for each species, because within-species samples were limited to only a few samples. Evolutionary models are particularly affected by measurement error (Silvestro et al., Reference Silvestro, Kostikova, Litsios, Pearman and Salamin2015). Hence, we estimated the pooled variance across the species and used it, weighted by sample size, to estimate the sampling variance of the individual species (see Garamszegi, Reference Garamszegi2014). All data were log10 transformed (Beaulieu et al., Reference Beaulieu, Jhwueng, Boettiger and O'Meara2012).

A phylogenetic tree was compiled by pruning from the GBMB mega-tree (GenBank taxa with a backbone provided by Magallón et al., Reference Magallón, Gómez-Acevedo, Sánchez-Reyes and Hernández-Hernández2015) of seed plants (Smith and Brown, Reference Smith and Brown2018), the 3242 angiosperm species present in our dataset. As a measure of the phylogenetic signal, we applied Pagel's λ (Pagel, Reference Pagel1999). A significant phylogenetic signal of trait states on the phylogenetic tree occurs when λ > 0, meaning taxa are more similar than expected by chance.

Models of trait evolution

To determine the evolutionary correlations and whether the evolution of seed mass and GS differed among the three life forms (representing the selective regimes), different multivariate models of trait evolution were fitted (Table 1). Two main classes of evolutionary models were applied: the BM and the OU process models. BM models estimate the stochastic evolution of a continuously valued trait through time (controlled by the drift rate parameter σ2). They can approximate various scenarios of phenotypic evolution such as drift (Felsenstein, Reference Felsenstein1988; Hansen, Reference Hansen1997; O'Meara et al., Reference O'Meara, Ané, Sanderson and Wainwright2006). In contrast, the OU models estimate trait selection toward a common optimal value and add to the BM model a parameter α that determines the strength of selection toward an optimal trait θ (Hansen, Reference Hansen1997; Butler and King, Reference Butler and King2004; Beaulieu et al., Reference Beaulieu, Jhwueng, Boettiger and O'Meara2012).

Table 1. Performance of the multivariate evolutionary models fitted on seed mass and GS (1C or 1Cx) in angiosperms

The best-fitting model, based on Akaike weights, was the OUM, which estimated a separate θ (evolutionary optimum) for each life form. σ2 represents the evolutionary drift rate (rate of stochastic motion)

Abbreviations: BM, Brownian motion models; OU, Ornstein–Uhlenbeck models.

For each main class of evolutionary models (BM and OU), we fitted two versions, for a total of four different models (Table 1): for BM models, we fitted a model with one drift rate for the whole tree (BM1) and a model with one drift rate per life-form regime (BMM). We also fitted different variants of the OU models (Beaulieu et al., Reference Beaulieu, Jhwueng, Boettiger and O'Meara2012): with a single optimum θ (OU1) or with a different optimum for each life form (OUM). In all cases, the starting value was assumed to be distributed according to the stationary distribution of the OU process (Clavel et al., Reference Clavel, Escarguel and Merceron2015). All analyses were carried out in R (R Development Core Team, 2020), using the mvMORPH package (Clavel et al., Reference Clavel, Escarguel and Merceron2015).

Each species was assigned to a life form (annual, perennial herb, woody) based on TRY v5 (https://www.try-db.org; Kattge et al., Reference Kattge, Bönisch, Díaz, Lavorel, Prentice, Leadley and Cuntz2020), the Plant DNA C-values database (Pellicer and Leitch, 2019) and on the woodiness database (FitzJohn et al., Reference FitzJohn, Pennell, Zanne, Stevens, Tank and Cornwell2014). Internal branches were assigned to each discrete category (annual, perennial herb, woody) using stochastic character mapping. The best transition model was first selected by comparing the AICc of three models fitted with the R package ape (Paradis et al., Reference Paradis, Claude and Strimmer2008): the EqualRate (ER; AICc = 4372), Symmetric (SYM; AICc = 3961) and All Rates Different (ARD; AICc = 3782) were fitted to reconstruct ancestral states in life forms. We then generated 100 stochastic maps (R package phytools; Revell, Reference Revell2012), based on the best transition model (ARD), assuming different transition rates between character states. We used stochastic maps in order to consider the effect of uncertainty in the evolutionary history of selective regimes on the tree.

The reliability of the parameter estimates returned by the models was evaluated by checking that the eigenvalues of the Hessian were positive (Clavel et al., Reference Clavel, Escarguel and Merceron2015). The AIC weight (wi), representing the relative likelihood that model i is the best-fitting model given a set of models (Burnham and Anderson, Reference Burnham and Anderson2002), was calculated for all models.

Results

Mean seed mass and GS values in life forms

Mean seed mass observed in the dataset was 15.09 mg (11.80–20.00, 95%CI) for annual herbs, 21.80 mg (0.16–43.50, 95%CI) for perennial herbs and 1001.25 mg (16.24–1986.27, 95%CI) for woody plants. Mean GS (1C) observed in the dataset was 2.67 pg (2.42–2.92, 95%CI) for annual herbs, 5.01 pg (4.61–5.42, 95%CI) for perennial herbs and 1.79 pg (1.50–2.06, 95%CI) for woody plants. Mean monoploid GS (1Cx) observed in the dataset was 2.25 pg (2.05–2.44, 95%CI) for annual herbs, 4.81 pg (4.30–5.32, 95%CI) for perennial herbs and 1.51 pg (1.29–1.73, 95%CI) for woody plants.

Phylogenetic signal

A significant phylogenetic signal was observed in both traits with λ = 0.96 (0.95–0.97, 95%CI) for seed mass, λ = 0.92 (0.91–0.93, 95%CI) for 1C and λ = 0.97 (0.97–0.98, 95%CI) for 1Cx. This indicates that closely related species have very similar seed mass and GS.

Models of seed mass and GS evolution

The multivariate analyses supported OUM as the best-fitting model for both seed mass-1C GS and seed mass-1Cx GS (AICc weight = 1; Table 1). This model suggests that the seed mass and GS have different evolutionary optima (θ) for the three life forms and that there is an evolutionary force that maintains seed mass and GS closer to these evolutionary optima than would be expected under a pure drift scenario (BM model).

The estimated parameters as medians across 100 stochastic maps are reported in Table 2. The evolutionary optimal seed mass towards which species evolved was higher for woody plants (back-transformed median = 40.87 mg) than in perennial (back-transformed median = 2.27 mg) and annual herbs (back-transformed median = 0.95 mg). However, the estimated optimal seed mass values for perennials and annuals are partially overlapping (Fig. 1) because estimated optimum values for annuals are less identifiable. The optimum GS (1C) is instead highest in perennial herbs (back-transformed median = 2.4 pg) and lowest in woody plants (back-transformed median = 1.04 pg), albeit largely overlapping with annuals (back-transformed median = 1.06 pg; Fig. 1).

Fig. 1. Evolutionary optima (θ) estimated from the multivariate OUM model. θ values are the estimated trait optima towards which 1C GS (pg) and seed mass (mg) evolve under different selective regimes (life forms): annuals (yellow), perennial herbs (green) and woody plants (brown). The dashed lines represent the median θ for each category. Each dot as well as the probability density distributions of optimal GS and seed mass were generated by running the analyses on 100 stochastic maps representing the effect of the uncertainty in reconstructing the ancestral states of life-form regimes and mapping them on the phylogenetic tree.

Table 2. Model parameters for the multivariate OUM model, which was the model that received the highest AICc weight (Table 1)

Estimated values of the parameters θ (evolutionary optimum), α (selective pull), σ2 (rate of stochastic motion), phylogenetic half-life (t 1/2 = ln(2)/α) and stationary variance (vy = σ2/2α) are shown. Parameter estimates are reported as median across 100 stochastic maps; numbers in brackets indicate the 25% and the 75% quantiles.

The phylogenetic half-life t 1/2 is longer for seed mass as compared with GS; accordingly, the selection strength estimate (α) is much higher in GS (Table 2) suggesting that GS changes towards the respective optima should happen more rapidly than seed mass changes when shifting from one life form to another. However, the estimated stationary variance and the stochasticity component (σ2) for GS were higher as compared with that of seed mass (Table 2), also indicating stronger random changes in GS.

The overall evolutionary correlation (r) between seed mass and 1C GS was moderate (0.12) while the one between seed mass and 1Cx GS was low (0.01). The evolutionary correlation was instead stronger within life forms, particularly in annual plants (0.54; Table 3).

Table 3. Evolutionary correlations (r) between seed mass and GS (1C and 1Cx)

Estimates are reported as mean across 100 stochastic maps; numbers in brackets indicate the 25% and the 75% quantiles

Discussion

Using multivariate evolutionary models on data from 3242 species, we showed an overall positive correlated evolution of seed mass and GS, deviating from a pure drift process. As we will outline below, there is strong evidence that evolutionary changes in seed and genome sizes were driven by adaptive selection towards optimal values differing among life forms. Specifically, evolutionary correlation is strongest in annual plants, suggesting that the two traits are tightly adaptively related in this group of plants, likely ensuring high regenerative potential.

The evolutionary optima towards which seed mass and GS evolve show a covariation toward small values in annuals, intermediate values in perennial herbs and a trade-off between seed mass and GS in woody plants. These results confirm our expectations and should be interpreted as functionally linked with different net effects on fitness (Laughlin et al., Reference Laughlin, Gremer, Adler, Mitchell and Moore2020) among life forms (Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005; Veselý et al., Reference Veselý, Bureš, Šmarda and Pavlíček2012; Shao et al., Reference Shao, Li, Luo, Wang, Xi, Liu and Xu2021) which occupy different positions in the plant life spectrum (Díaz et al., Reference Díaz, Kattge, Cornelissen, Wright, Lavorel, Dray and Gorné2016; Laughlin et al., Reference Laughlin, Gremer, Adler, Mitchell and Moore2020).

Estimated optimum seed mass values for annuals partially overlap with optimum values estimated for perennial herbs. Indeed, the selective pull (α) was lower for seed mass and the phylogenetic half-life (corresponding to the time required for the expected phenotype to move half-way toward the optimal shape from its ancestral state; Hansen, Reference Hansen1997) was longer as compared to GS, suggesting a stronger degree of phylogenetic constraint in the evolution of seed mass. Whilst the shorter phylogenetic half-life and stronger selective pull for GS can imply a strong selective pressure, the stationary variance (a measure of the relative influence of stochastic factors in the adaptive process) is also large, thus rapid changes in genome sizes may also occur as a consequence of other factors like unmeasured selective forces and genetic drift. In summary, it appears that the evolution of seed mass and GS follow a concerted evolutionary scenario mediated by life form, but it also seems that seed mass exhibits greater phylogenetic inertia compared to GS; the latter appearing much more labile. The evolutionary lability found here, particularly applies to 1C GS, likely as a consequence of rapid ploidy changes that occurred along lineages (Carta et al., Reference Carta, Bedini and Peruzzi2020). Nevertheless, the shorter phylogenetic half-life and the stronger selective pull in 1Cx compared to seed mass, still highlights a role of the basal monoploid genome quantity, irrespective of the ploidy level, in driving the observed patterns. Taken together, this empirical evidence helps understanding correlations between GS and plant traits. Nevertheless, more research is needed to separate the effects of GS from other factors influencing plant growth and fitness.

The current implementation does not allow the estimation of regime-specific selective pull (α) and drift rate (σ2) under the multivariate OUM model (Clavel et al., Reference Clavel, Escarguel and Merceron2015), unlike the univariate framework (Beaulieu et al., Reference Beaulieu, Jhwueng, Boettiger and O'Meara2012). Nevertheless, our results already suggest the occurrence of different degrees of selection in different life forms. Indeed, whilst the overall evolutionary correlation between seed mass and GS was weak, the evolutionary correlation was stronger within life forms, particularly in annual plants, suggesting that the two traits are tightly adaptively related at the seed level in this functional group of plants. This could be to ensure life cycle completion within a restricted growing season (Stebbins, Reference Stebbins1938; Grant, Reference Grant1958; Harper, Reference Harper1977; Baskin and Baskin, Reference Baskin and Baskin2014), with a corresponding positive net effect on fitness (Laughlin et al., Reference Laughlin, Gremer, Adler, Mitchell and Moore2020). In contrast, the evolutionary correlation between seed mass and GS was weaker in woody plants. Different reasons could be considered to explain this weaker correlation. First, it should be noted that the larger seed mass optimum found in woody plants is not a direct consequence of woodiness itself, but is likely to reflect the positive association with plant height (Moles et al., Reference Moles, Ackerly, Webb, Tweddle, Dickie, Pitman and Westoby2005). Then, we should consider that the positive effects of possessing larger seeds are not necessarily linked to the net effect on fitness, while the small GS, which is directly associated with vessel diameter, may have much more impact on demographic rate (such as survival or reproduction; Adler et al., Reference Adler, Salguero-Gómez, Compagnoni, Hsu, Ray-Mukherjee, Mbeau-Ache and Franco2014; Laughlin et al., Reference Laughlin, Gremer, Adler, Mitchell and Moore2020). In addition, although we found that GS is generally under selective constraints, life-history specific constraints are also present. For example, in woody plants, these constraints likely reflect the longer generation times that characterize them (Beaulieu et al., Reference Beaulieu, Smith and Leitch2010), providing fewer opportunities for changes in GS to occur per unit of time. Altogether, the weak evolutionary correlation between seed mass and GS in woody plants points toward a mismatch between the effects of seed mass and GS among developmental stages, with seed mass that is an important trait early in the life cycles, while specifically for woody plants GS is a major constraint at later stages (xylem diameter restrictions with negative effects on GS; Knight and Beaulieu, Reference Knight and Beaulieu2008).

We conclude that the evolutionary correlation between seed mass and GS is present but weaker than previously thought because this relation is strongly mediated by plant life forms. The asymmetry in the correlated evolution acting on seed and genome sizes due to life form could explain how life-history traits interplay with functional trait and how plants have evolved diverse successful life-history strategies, under prevailing environmental conditions (Adler et al., Reference Adler, Salguero-Gómez, Compagnoni, Hsu, Ray-Mukherjee, Mbeau-Ache and Franco2014; Liu et al., Reference Liu, Walck, El-Kassaby and Jimenez-Lopez2017; Lundgren and Das Marais, Reference Lundgren and Des Marais2020).

The findings of this work can help to predict the functional responses of plant traits and their prevalence in response to current and future climate change (Baskin and Baskin, Reference Baskin and Baskin2022; Carta et al., Reference Carta, Fernández-Pascual, Gioria, Müller, Rivière, Rosbakh, Saatkamp, Vandelook and Mattana2022). Moreover, understanding how life-history and functional seed traits interplay may support the potential domestication process of yet to be explored wild plants, unlocking their potential economic, nutritional, medicinal and cultural value (Mattana et al., Reference Mattana, Ulian and Pritchard2022). However, because the relationship between GS and other plant traits increases at lower phenotypic scales and the strength of such relations varies between cell types and developmental stages (Knight and Beaulieu, Reference Knight and Beaulieu2008), future studies relating GS and seed traits should be encouraged, especially concerning seed functional traits directly linked to cell cycles and/or cell expansions like embryo growth and germination (Astuti et al., Reference Astuti, Pratesi, Peruzzi and Carta2020).

Acknowledgements

All analyses were performed in the high-performance computing cluster at the University of Pisa.

Author contribution

A.C. conceived the study and performed the analyses. A.C. wrote the manuscript with help from F.V. A.C. prepared the figure with help from E.M. All authors revised the manuscript and approved the final version.

Conflicts of interest

The authors declare none.

References

Adler, PB, Salguero-Gómez, R, Compagnoni, A, Hsu, JS, Ray-Mukherjee, J, Mbeau-Ache, C and Franco, M (2014) Functional traits explain variation in plant life history strategies. Proceedings of the National Academy of Sciences 111, 740745.CrossRefGoogle ScholarPubMed
Astuti, G, Pratesi, S, Peruzzi, L and Carta, A (2020) Two closely related Tulipa species with different ploidy levels show distinct germination rates. Seed Science Research 30, 4548.CrossRefGoogle Scholar
Bainard, JD, Bainard, LD, Henry, TA, Fazekas, AJ and Newmaster, SG (2012) A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits. New Phytologist 196, 12401250.CrossRefGoogle ScholarPubMed
Baskin, CC and Baskin, JM (2014) Seeds: ecology, biogeography, and evolution of dormancy and germination. San Diego, CA, Academic Press.Google Scholar
Baskin, CC and Baskin, JM (2022) Plant regeneration from seeds: a global warming perspective. San Diego, CA, Academic Press.Google Scholar
Beaulieu, JM, Moles, AT, Leitch, IJ, Bennett, MD, Dickie, JB and Knight, CA (2007) Correlated evolution of genome size and seed mass. New Phytologist 173, 422437.CrossRefGoogle ScholarPubMed
Beaulieu, JM, Smith, SA and Leitch, IJ (2010) On the tempo of genome size evolution in angiosperms. Journal of Botany. https://doi.org/10.1155/2010/989152CrossRefGoogle Scholar
Beaulieu, JM, Jhwueng, DC, Boettiger, C and O'Meara, BC (2012) Modeling stabilizing selection: expanding the Ornstein–Uhlenbeck model of adaptive evolution. Evolution 66, 23692383.CrossRefGoogle ScholarPubMed
Bennett, MD (1972) Nuclear DNA content and minimum generation time in herbaceous plants. Proceedings of the Royal Society of London. Series B. Biological Sciences 181, 109135.Google ScholarPubMed
Bennett, MD (1987) Variation in genomic form in plants and its ecological implications. New Phytologist 106, 177200.CrossRefGoogle Scholar
Bolmgren, K and Eriksson, O (2010) Seed mass and the evolution of fleshy fruits in angiosperms. Oikos 119, 707718.CrossRefGoogle Scholar
Burnham, KP and Anderson, DR (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2nd edn. Springer Verlag, New York, NY.Google Scholar
Butler, MA and King, AA (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. The American Naturalist 164, 683695.CrossRefGoogle ScholarPubMed
Carta, A and Peruzzi, L (2016) Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae. New Phytologist 210, 709716.CrossRefGoogle ScholarPubMed
Carta, A, Bedini, G and Peruzzi, L (2020) A deep dive into the ancestral chromosome number and genome size of flowering plants. New Phytologist 228, 10971106.CrossRefGoogle ScholarPubMed
Carta, A, Fernández-Pascual, E, Gioria, M, Müller, JV, Rivière, S, Rosbakh, S, Saatkamp, A, Vandelook, F and Mattana, E (2022) Climate shapes the seed germination niche of temperate flowering plants: a meta-analysis of European seed conservation data. Annals of Botany. https://doi.org/10.1093/aob/mcac037CrossRefGoogle ScholarPubMed
Chen, SC, Poschlod, P, Antonelli, A, Liu, U and Dickie, JB (2020) Trade-off between seed dispersal in space and time. Ecology Letters 23, 16351642.CrossRefGoogle ScholarPubMed
Clavel, J, Escarguel, G and Merceron, G (2015) mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data. Methods in Ecology and Evolution 6, 13111319.CrossRefGoogle Scholar
Díaz, S, Kattge, J, Cornelissen, JH, Wright, IJ, Lavorel, S, Dray, S and Gorné, LD (2016) The global spectrum of plant form and function. Nature 529, 167171.CrossRefGoogle ScholarPubMed
Eriksson, O, Friis, EM and Löfgren, P (2000) Seed size, fruit size, and dispersal systems in angiosperms from the early cretaceous to the late tertiary. The American Naturalist 156, 4758.CrossRefGoogle Scholar
Faizullah, L, Morton, JA, Hersch-Green, EI, Walczyk, AM, Leitch, AR and Leitch, IJ (2021) Exploring environmental selection on genome size in angiosperms. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2021.06.001CrossRefGoogle ScholarPubMed
Felsenstein, J (1988) Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19, 445471.CrossRefGoogle Scholar
FitzJohn, RG, Pennell, MW, Zanne, AE, Stevens, PF, Tank, DC and Cornwell, WK (2014) How much of the world is woody? Journal of Ecology 102, 12661272.CrossRefGoogle Scholar
Garamszegi, LZ (2014) Modern phylogenetic comparative methods and their application in evolutionary biology: concepts and practice. Springer Berlin.CrossRefGoogle Scholar
Gioria, M, Pyšek, P, Baskin, CC and Carta, A (2020) Phylogenetic relatedness mediates persistence and density of soil seed banks. Journal of Ecology 108, 21212131.CrossRefGoogle Scholar
Grant, VE (1958) The regulation of recombination in plants. Cold Spring Harbor Symposia on Quantitative Biology 23, 337363.CrossRefGoogle ScholarPubMed
Hansen, TF (1997) Stabilizing selection and the comparative analysis of adaptation. Evolution 51, 13411351.CrossRefGoogle ScholarPubMed
Harper, JL (1977) Population biology of plants. London, Academic Press.Google Scholar
Howe, HF and Smallwood, J (1982) Ecology of seed dispersal. Annual Review of Ecology and Systematics 13, 201228.CrossRefGoogle Scholar
Igea, J, Miller, EF, Papadopulos, AS and Tanentzap, AJ (2017) Seed size and its rate of evolution correlate with species diversification across angiosperms. PLoS Biology 15, e2002792.CrossRefGoogle ScholarPubMed
Kattge, J, Bönisch, G, Díaz, S, Lavorel, S, Prentice, IC, Leadley, P and Cuntz, M (2020) TRY plant trait database-enhanced coverage and open access. Global Change Biology 26, 119188.CrossRefGoogle ScholarPubMed
Knight, CA and Beaulieu, JM (2008) Genome size scaling through phenotype space. Annals of Botany 101, 759766.CrossRefGoogle ScholarPubMed
Knight, CA, Molinari, NA and Petrov, DA (2005) The large genome constraint hypothesis: evolution, ecology and phenotype. Annals of Botany 95, 177190.CrossRefGoogle ScholarPubMed
Laughlin, DC, Gremer, JR, Adler, PB, Mitchell, RM and Moore, MM (2020) The net effect of functional traits on fitness. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2020.07.010CrossRefGoogle ScholarPubMed
Leitch, IJ and Bennett, MD (2007) Genome size and its uses: the impact of flow cytometry, pp. 153176 in Doležel, J et al. (Eds) Flow cytometry with plant cells: analysis of genes, chromosomes and genomes, Weinheim, Wiley-VCH Verlag.CrossRefGoogle Scholar
Linkies, A, Graeber, K, Knight, C and Leubner-Metzger, G (2010) The evolution of seeds. New Phytologist 186, 817831.CrossRefGoogle ScholarPubMed
Liu, Y, Walck, JL and El-Kassaby, YA (2017) Roles of the environment in plant life-history trade-offs, in Jimenez-Lopez, JC (Ed.) Seed biology, London, InTechOpen, 324.Google Scholar
Long, RL, Gorecki, MJ, Renton, M, Scott, JK, Colville, L, Goggin, DE and Finch-Savage, WE (2015) The ecophysiology of seed persistence: a mechanistic view of the journey to germination or demise. Biological Reviews 90, 3159.CrossRefGoogle ScholarPubMed
Lundgren, MR and Des Marais, DL (2020) Life history variation as a model for understanding trade-offs in plant–environment interactions. Current Biology 30, R180R189.CrossRefGoogle ScholarPubMed
Magallón, S, Gómez-Acevedo, S, Sánchez-Reyes, LL and Hernández-Hernández, T (2015) A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytologist 207, 437453.CrossRefGoogle ScholarPubMed
Mattana, E, Ulian, T and Pritchard, HW (2022) Seeds as natural capital. Trends in Plant Science 27, 139146.CrossRefGoogle ScholarPubMed
Moles, AT and Westoby, M (2004) Seedling survival and seed size: a synthesis of the literature. Journal of Ecology 92, 372383.CrossRefGoogle Scholar
Moles, AT, Ackerly, DD, Webb, CO, Tweddle, JC, Dickie, JB, Pitman, AJ and Westoby, M (2005) Factors that shape seed mass evolution. Proceedings of the National Academy of Sciences 102, 1054010544.CrossRefGoogle ScholarPubMed
O'Meara, BC, Ané, C, Sanderson, MJ and Wainwright, PC (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution 60, 922933.CrossRefGoogle ScholarPubMed
Pagel, M (1999) Inferring the historical patterns of biological evolution. Nature 401, 877884.CrossRefGoogle ScholarPubMed
Paradis, E, Claude, J and Strimmer, K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289290.CrossRefGoogle ScholarPubMed
Pellicer, J, Hidalgo, O, Dodsworth, S and Leitch, IJ (2018) Genome size diversity and its impact on the evolution of land plants. Genes 9, 88.CrossRefGoogle ScholarPubMed
Pellicer, J and Leitch, IJ (2020) The plant DNA c-values database (release 7.1): an updated online repository of plant genome size data for comparative studies. New Phytologist 226, 301305.CrossRefGoogle ScholarPubMed
Price, HJ (1988) DNA content variation among higher plants. Annals of the Missouri Botanical Garden 75, 12481257.CrossRefGoogle Scholar
R Core Team (2020) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
Revell, LJ (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in ecology and evolution 2, 217223.CrossRefGoogle Scholar
Royal Botanic Gardens Kew (2022) Seed Information Database (SID). Version 7.1. Available from: http://data.kew.org/sid/ (May 2022)Google Scholar
Shao, C, Li, Y, Luo, A, Wang, Z, Xi, Z, Liu, J and Xu, X (2021) Relationship between functional traits and genome size variation of angiosperms with different life forms. Biodiversity Science 29, 575.CrossRefGoogle Scholar
Silvestro, D, Kostikova, A, Litsios, G, Pearman, PB and Salamin, N (2015) Measurement errors should always be incorporated in phylogenetic comparative analysis. Methods in Ecology and Evolution 6, 340346.CrossRefGoogle Scholar
Simonin, KA and Roddy, AB (2018) Genome downsizing, physiological novelty, and the global dominance of flowering plants. PLoS Biology 16, e2003706.CrossRefGoogle ScholarPubMed
Šímová, I and Herben, T (2012) Geometrical constraints in the scaling relationships between genome size, cell size and cell cycle length in herbaceous plants. Proceedings of the Royal Society B: Biological Sciences 279, 867875.CrossRefGoogle ScholarPubMed
Sims, HJ (2013) Morphological rates of angiosperm seed size evolution. Evolution 67, 13381346.Google ScholarPubMed
Smith, SA and Brown, JW (2018) Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany 105, 302314.CrossRefGoogle ScholarPubMed
Stebbins, GL (1938) Cytological characteristics associated with the different growth habits in the dicotyledons. American Journal of Botany 25, 189198.CrossRefGoogle Scholar
Thompson, KB, Band, SR and Hodgson, JG (1993) Seed size and shape predict persistence in soil. Functional ecology 7, 236241.CrossRefGoogle Scholar
Verdú, M (2002) Age at maturity and diversification in woody angiosperms. Evolution 56, 13521361.CrossRefGoogle ScholarPubMed
Veselý, P, Bureš, P, Šmarda, P and Pavlíček, T (2012) Genome size and DNA base composition of geophytes: the mirror of phenology and ecology? Annals of Botany 109, 6575.CrossRefGoogle ScholarPubMed
Figure 0

Table 1. Performance of the multivariate evolutionary models fitted on seed mass and GS (1C or 1Cx) in angiosperms

Figure 1

Fig. 1. Evolutionary optima (θ) estimated from the multivariate OUM model. θ values are the estimated trait optima towards which 1C GS (pg) and seed mass (mg) evolve under different selective regimes (life forms): annuals (yellow), perennial herbs (green) and woody plants (brown). The dashed lines represent the median θ for each category. Each dot as well as the probability density distributions of optimal GS and seed mass were generated by running the analyses on 100 stochastic maps representing the effect of the uncertainty in reconstructing the ancestral states of life-form regimes and mapping them on the phylogenetic tree.

Figure 2

Table 2. Model parameters for the multivariate OUM model, which was the model that received the highest AICc weight (Table 1)

Figure 3

Table 3. Evolutionary correlations (r) between seed mass and GS (1C and 1Cx)