Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

Abstract

In response to our paper on the evolutionary history of the Chinese flora, Qian suggests that certain features of the divergence time estimation employed might have led to biased conclusions in Lu et al (2018). Here, we consider Qian's specific criticisms, explore the extent of uncertainty in the data and demonstrate that (i) no systematic bias toward dates that are too young or too old is detected in Lu et al.; (ii) constraint of the crown age of angiosperms does not bias the generic ages estimated by Lu et al.; and (iii) ages derived from the Chinese regional phylogeny do not bias the conclusions reported by Lu et al. All these analyses confirm that the conclusions reported previously are robust. We argue that, like many large-scale biodiversity analyses, sources of noise in divergence time estimation are to be expected, but these should not be confused with bias. In response to our paper on the evolutionary history of the flora of China, Qian (2019) suggests that the molecular-based estimates of divergence times may have substantially biased our conclusions (Lu et al., 2018). Although Qian (2019) notes some issues in divergence time estimation that the community also has raised (e.g. discordance between molecular estimates and the fossil record; the influence of incomplete phylogeny on divergence time estimation), some of his statements are misleading, and there is no evidence supporting his statement that the conclusions in Lu et al. (2018) are biased. Here, we consider Qian's specific criticisms, explore the potential uncertainty in our data, reanalyse the data with different constraints and address Qian's concerns on three major aspects below.

Should we be concerned about incomplete taxon sampling when assessing the evolutionary history of regional biotas?

“…In conclusion, we concur with Lu et al (2020) in that regional phylogenies are useful to assess divergence times as long as they represent taxon-rich biotas and comparisons are conducted within regions and in a relative manner. Otherwise, the reliability of the contrasts is not guaranteed given that (1) regional phylogenies produce consistent biases towards age overestimation, (2) the correlation between regional and actual ages may be weak in taxon-poor regions and (3) among-region comparisons could be misleading because differences in divergence times may appear greater than they are regardless of taxon richness.…”

“…Specifically, Qian (2019) pointed out that incomplete taxon sampling inherent in regional phylogenies may produce biases towards divergence time overestimation for any genus, thus questioning the reliability of regional phylogenies to conduct such inferences. While Lu et al (2020) adhered to the conclusions of their study, they acknowledged that the impact of incomplete taxon sampling on divergence time estimations remains to be assessed directly. Here, we follow up the open debate between Qian (2019) and Lu et al (2020) to fill in this gap of knowledge; should we be concerned about incomplete taxon sampling when assessing the evolutionary history of regional biotas?…”

“…While Lu et al (2020) adhered to the conclusions of their study, they acknowledged that the impact of incomplete taxon sampling on divergence time estimations remains to be assessed directly. Here, we follow up the open debate between Qian (2019) and Lu et al (2020) to fill in this gap of knowledge; should we be concerned about incomplete taxon sampling when assessing the evolutionary history of regional biotas? First, we drew the global distribution of all the genera sampled in the mega-tree GBOTB.extended, which is the most comprehensive time-calibrated molecular phylogeny for vascular plants published hitherto (Jin & Q ian, 2019).…”

“…Qian (2019) point out that the relatively low correlation between genus ages in the purpose-built regional phylogeny of Lu et al (2018) and those in the global phylogeny of Zanne et al (2014, Pearson's r = 0.58) questions the reliability of Lu et al's (2018) analyses. Lu et al (2020) adhered to the conclusions of their study, but they did not explicitly elucidate the differential contribution of the potential sources of noise in their divergence time estimates. Our results suggest that the relatively low correlation reported by Qian (2019) can be largely attributed to differences in the calibration methods between both studies rather than the effect of incomplete taxon sampling, given the great richness of taxa in the Chinese angiosperm flora (~22% of the angiosperm genera of the world are native to this region; Christenhusz & Byng, 2016).…”

Historical biogeography of Tetrastigma (Vitaceae): Insights into floristic exchange patterns between Asia and Australia

“…(2011b). The discrepancy is most likely caused by differences in taxon sampling, because failing to sample the close relatives of a clade may lead to an over‐estimation of the stem age, while incomplete sampling within a clade may lead to an under‐estimation of crown age for that clade (Lu et al., 2020). Previous studies generally took the divergence time between Tetrastigma and Causonis (formerly Cayratia subg.…”