Jurriaan M. de Vos

Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event

Cyanobacteria are among the most diverse prokaryotic phyla, with morphotypes ranging from unicellular to multicellular filamentous forms, including those able to terminally (i.e., irreversibly) differentiate in form and function. It has been suggested that cyanobacteria raised oxygen levels in the atmosphere around 2.45–2.32 billion y ago during the Great Oxidation Event (GOE), hence dramatically changing life on the planet. However, little is known about the temporal evolution of cyanobacterial lineages, and possible interplay between the origin of multicellularity, diversification of cyanobacteria, and the rise of atmospheric oxygen. We estimated divergence times of extant cyanobacterial lineages under Bayesian relaxed clocks for a dataset of 16S rRNA sequences representing the entire known diversity of this phylum. We tested whether the evolution of multicellularity overlaps with the GOE, and whether multicellularity is associated with significant shifts in diversification rates in cyanobacteria. Our results indicate an origin of cyanobacteria before the rise of atmospheric oxygen. The evolution of multicellular forms coincides with the onset of the GOE and an increase in diversification rates. These results suggest that multicellularity could have played a key role in triggering cyanobacterial evolution around the GOE.

Estimating the normal background rate of species extinction

A key measure of humanitys global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher.

Heterostyly accelerates diversification via reduced extinction in primroses

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwins model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.

Decrease of sexual organ reciprocity between heterostylous primrose species, with possible functional and evolutionary implications

BACKGROUND AND AIMS Heterostyly is a floral polymorphism that has fascinated evolutionary biologists since Darwins seminal studies on primroses. The main morphological characteristic of heterostyly is the reciprocal placement of anthers and stigmas in two distinct (distyly) floral morphs. Variation in the degree of intermorph sexual reciprocity is relatively common and known to affect patterns of pollen transfer within species. However, the partitioning of sexual organ reciprocity within and between closely related species remains unknown. This study aimed at testing whether intermorph sexual reciprocity differs within vs. between primrose species that hybridize in nature and whether the positions of sexual organs are correlated with other floral traits. METHODS Six floral traits were measured in both floral morphs of 15 allopatric populations of Primula elatior, P. veris and P. vulgaris, and anther-stigma reciprocity was estimated within and between species. A combination of univariate and multivariate approaches was used to test whether positions of reproductive organs were less reciprocal between than within species, to assess correlations between sexual organ positions and other corolla traits, and to quantify differences between morphs and species. KEY RESULTS The three species were morphologically well differentiated in most floral traits, except that P. veris and P. vulgaris did not differ significantly in sexual organ positions. Overall, lower interspecific than intraspecific sexual organ reciprocity was detected. This decrease was marked between P. elatior and P. vulgaris, intermediate and variable between P. elatior and P. veris, but negligible between P. veris and P. vulgaris. CONCLUSIONS Differences in anther and stigma heights between the analysed primrose species were of the same magnitude or larger than intraspecific differences that altered pollen flow within other heterostylous systems. Therefore, it is possible to suggest that considerable reductions of sexual organ reciprocity between species may lower interspecific pollen flow, with potential effects on reproductive isolation.

Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species

The type section of Primula (Primulaceae), here considered to include seven species, is phylogenetically quite isolated in its genus. Although its species are popular ornamentals, traditional medicinal plants and model organisms for the study of heterostyly, the section has not yet been studied from a phylogenetic or evolutionary perspective. Using phylogenetic analysis of nuclear ITS and plastid data from all species and subspecies, we find that widespread Primula elatior is genetically heterogeneous and non-monophyletic to most if not all of the other ingroup taxa. The Genealogical Sorting Index (GSI) indicates that the assumption of all currently accepted species being independent lineages is consistent with the data. It is possible that P. elatior in its current circumscription may represents the disjointed remnant of an ancestral species from which the other recognized species diverged. However, based on available data, the alternative possibility of introgression explaining the non-monophyly of this species cannot be excluded. Species trees show P. elatior and P. veris as sister species. Primula vulgaris and P. juliae are closely related, while, in contrast to previous assumptions, P. renifolia does not appear to be a close relative of P. megaseifolia. With the sections isolation from the rest of the genus and very short internal branches, our dataset also presents a case study of the confounding effects of different branch length priors on the Bayesian estimation of resulting branch length estimates. Experimental runs using different priors confirm the problem of resulting estimates varying by orders of magnitude, while topology and relative branch lengths seem unaffected.

Small and ugly? Phylogenetic analyses of the "selfing syndrome" reveal complex evolutionary fates of monomorphic primrose flowers.

One of the most common trends in plant evolution, loss of self‐incompatibility and ensuing increases in selfing, is generally assumed to be associated with a suite of phenotypic changes, notably a reduction of floral size, termed the selfing syndrome. We investigate whether floral morphological traits indeed decrease in a deterministic fashion after losses of self‐incompatibility, as traditionally expected, using a phylogeny of 124 primrose species containing nine independent transitions from heterostyly (heteromorphic incompatibility) to homostyly (monomorphic self‐compatibility), a classic system for evolution of selfing. We find similar overall variability of homostylous and heterostylous species, except for diminished herkogamy in homostyles. Bayesian mixed models demonstrate differences between homostylous and heterostylous species in all traits, but net effects across species are small (except herkogamy) and directionality differs among traits. Strongly drift‐like evolutionary trajectories of corolla tube length and corolla diameter inferred by Ornstein–Uhlenbeck models contrast with expected deterministic trajectories toward small floral size. Lineage‐specific population genetic effects associated with evolution of selfing may explain that reductions of floral size represent one of several possible outcomes of floral evolution after loss of heterostyly in primroses. Contrary to the traditional paradigm, selfing syndromes may, but do not necessarily evolve in response to increased selfing.

Doubtful pathways to cold tolerance in plants.

arising from A. E. Zanne et al. 506, 89–92 (2014); doi:10.1038/nature12872Zanne et al. addressed an important evolutionary question: how did flowering plants repeatedly enter cold climates? Herbaceous growth, deciduous leaves, and narrow water-conducting cells are adaptations to freezing. Using phylogenetic analyses, they concluded that herbs and narrow conduits evolved first in the tropics (“trait first”), facilitating movement into freezing areas, but that deciduous leaves evolved in response to freezing temperatures (“climate first”). Unfortunately, even after correcting for an error that we uncovered, the “striking findings” of Zanne et al. seem inconclusive; here we highlight methodological issues of more general interest and question the value of their approach. There is a Reply to this Brief Communication Arising by Zanne, A. E. et al. Nature 521, http://dx.doi.org/10.1038/nature14394 (2015).

Both morph- and species-dependent asymmetries affect reproductive barriers between heterostylous species

Abstract The interaction between floral traits and reproductive isolation is crucial to explaining the extraordinary diversity of angiosperms. Heterostyly, a complex floral polymorphism that optimizes outcrossing, evolved repeatedly and has been shown to accelerate diversification in primroses, yet its potential influence on isolating mechanisms remains unexplored. Furthermore, the relative contribution of pre‐ versus postmating barriers to reproductive isolation is still debated. No experimental study has yet evaluated the possible effects of heterostyly on pre‐ and postmating reproductive mechanisms. We quantify multiple reproductive barriers between the heterostylous Primula elatior (oxlip) and P. vulgaris (primrose), which readily hybridize when co‐occurring, and test whether traits of heterostyly contribute to reproductive barriers in unique ways. We find that premating isolation is key for both species, while postmating isolation is considerable only for P. vulgaris; ecogeographic isolation is crucial for both species, while phenological, seed developmental, and hybrid sterility barriers are also important in P. vulgaris, implicating sympatrically higher gene flow into P. elatior. We document for the first time that, in addition to the aforementioned species‐dependent asymmetries, morph‐dependent asymmetries affect reproductive barriers between heterostylous species. Indeed, the interspecific decrease of reciprocity between high sexual organs of complementary floral morphs limits interspecific pollen transfer from anthers of short‐styled flowers to stigmas of long‐styled flowers, while higher reciprocity between low sexual organs favors introgression over isolation from anthers of long‐styled flowers to stigmas of short‐styled flowers. Finally, intramorph incompatibility persists across species boundaries, but is weakened in long‐styled flowers of P. elatior, opening a possible backdoor to gene flow through intramorph pollen transfer between species. Therefore, patterns of gene flow across species boundaries are likely affected by floral morph composition of adjacent populations. To summarize, our study highlights the general importance of premating isolation and newly illustrates that both morph‐ and species‐dependent asymmetries shape boundaries between heterostylous species.

A Tale of Two Morphs: Modeling Pollen Transfer, Magic Traits, and Reproductive Isolation in Parapatry

The evolution of the flower is commonly thought to have spurred angiosperm diversification. Similarly, particular floral traits might have promoted diversification within specific angiosperm clades. We hypothesize that traits promoting the precise positional transfer of pollen between flowers might promote diversification. In particular, precise pollen transfer might produce partial reproductive isolation that facilitates adaptive divergence between parapatric populations differing in their reproductive-organ positions. We investigate this hypothesis with an individual-based model of pollen transfer dynamics associated with heterostyly, a floral syndrome that depends on precise pollen transfer. Our model shows that precise pollen transfer can cause sexual selection leading to divergence in reproductive-organ positions between populations served by different pollinators, pleiotropically causing an increase in reproductive isolation through a “magic trait” mechanism. Furthermore, this increased reproductive isolation facilitates adaptive divergence between the populations in an unlinked, ecologically selected trait. In a different pollination scenario, however, precise pollen transfer causes a decrease in adaptive divergence by promoting asymmetric gene flow. Our results highlight the idea that magic traits are not “magic” in isolation; in particular, the effect size of magic traits in speciation depends on the external environment, and also on other traits that modify the strength of the magic traits influence on non-random mating. Overall, we show that the evolutionary consequences of pollen transfer dynamics can depend strongly on the available pollinator fauna and on the morphological fit between flowers and pollinators. Furthermore, our results illustrate the potential importance of even weak reproductive isolating barriers in facilitating adaptive divergence.

Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)

&NA; Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single‐copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi‐gene families. Here, we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (˜ 2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi‐gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75‐218 loci across 74 taxa, with ˜ 50% matrix completeness across data sets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent‐based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic‐scale data.