Node ages, relationships, and phylogenomic incongruence in an ancient gymnosperm lineage – Phylogeny of Ephedra revisited

Abstract

Knowledge of relationships among plants has improved dramatically but for many groups, it still rests solely on information from the plastid genome. Consequently, only parts of the organisms’ evolutionary history are revealed. For the ancient gymnosperms of Ephedra (Gnetales), previous conclusions were based on both plastid and nuclear ribosomal DNA data, but results were typically poorly resolved and supported, presumably because of information poverty in the utilized gene regions. With the aim of resolving phylogenetic questions using more data, we sequenced the plastid genome and the nuclear ribosomal cistron for 50 specimens of Ephedra, largely covering the diversity of the genus. Phylogeny and node ages were estimated using maximum likelihood and Bayesian methods. However, instead of clarifying a few remaining uncertainties, we were left with new questions and incongruent results. Age estimates of the crown group of Ephedra vary considerably depending on utilized software and specified tree prior. Furthermore, previous estimates of the phylogeny of Ephedra have largely reflected information from nrITS, despite utilization of plastid gene regions as well. With analyses based on the entire plastid genome, completely new results emerge. Earlier conclusions of deep divergences in the genus are not supported, and there are ample examples of phylogenetic incongruence. Our study overturns conclusions in previous work and highlights that we still know fairly little about evolution in the ancient Ephedra lineage. How many species of Ephedra are there, and how are they related? How old is the crown group? Many species appear affected by a history of hybridization/introgression and/or polyploidy, but other processes may result in similar patterns and reasons for the detected incongruences must be further analyzed, preferably using population‐level sampling and low‐copy nuclear data.

Integrative taxonomy tests possible hybridisation between Central Asian cerambycids (Coleoptera)

“…Namely, the Ephedra crown was dated to 30 Ma (Ickert‐Bond et al, 2009) or 32–8 Ma for extant taxa (Huang & Price, 2003), and thus the geological and hydrological events described took place at a time when modern Ephedra species prevailed in this region. However, according to more recent molecular inference (Rydin et al, 2021), the crown age was estimated as 100 Myr.…”

Not that young: combining plastid phylogenomic, plate tectonic and fossil evidence indicates a Palaeogene diversification of Cycadaceae

“…Previous studies have also documented that the branching process prior can substantially impact the age estimation for lineages that have undergone massive extinction [e.g. in cycads ( Condamine et al , 2015 ), Xanthorrhoea ( Crisp et al , 2014 ) and Ephedra ( Rydin et al , 2021 )], suggesting the tree prior effects are strongly dependent on data characteristics and the underlying phylogeny ( Ritchie et al , 2017 ). The Yule prior would, in general, be expected to yield an older age for the crown age compared to the birth–death prior because the Yule prior assumes a constant birth rate and zero extinction, resulting in nodes being more evenly spread over the tree ( Rydin et al , 2021 ).…”

“…in cycads ( Condamine et al , 2015 ), Xanthorrhoea ( Crisp et al , 2014 ) and Ephedra ( Rydin et al , 2021 )], suggesting the tree prior effects are strongly dependent on data characteristics and the underlying phylogeny ( Ritchie et al , 2017 ). The Yule prior would, in general, be expected to yield an older age for the crown age compared to the birth–death prior because the Yule prior assumes a constant birth rate and zero extinction, resulting in nodes being more evenly spread over the tree ( Rydin et al , 2021 ). Hence, the birth–death prior estimates more nodes toward the present compared to the past ( Gernhard, 2008 ), leading to a ‘pull to the present’ effect.…”

“…Given the above concerns, we recommend careful selection of both priors and fossils (or examined biogeographical events, if available) for internal calibration before inferring timescales of lineages that have undergone massive extinctions. Indeed, these cases indicate lineage age estimation will probably yield substantial gaps by using different priors or fossil combinations in BEAST ( Rydin et al , 2021 ).…”

Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales

“…However, the timescale for the evolution of Gnetales is higly uncertain. The oldest divergence, that of Gnetales and their closest relatives (Pinaceae or cupressophytes depending on the study), has been variously inferred to be dated between the Carboniferous and the Triassic (Hou et al, 2015;Ran et al, 2018), while the Gnetales crown age has been inferred to be between Late Triassic and the Early Cretaceous (Hou et al, 2015;Ran et al, 2018;Rydin et al, 2021). The divergence between Gnetum and Welwitschia is inferred to have occurred in the Early Cretaceous.…”