Three concerns have been raised by
Sánchez-Tójar et al . (2020) about our meta-analysis of
transgenerational effects (Yin et al . 2019): (1) the analysis did
not fully account for the non-independence among data, (2) the study
lacked transparency and the peer review was ineffective, and (3) the
literature search had limited coverage. These concerns are addressed
below.
First, Sánchez-Tójar et al . raised concerns regarding data
non-independence, and in their reanalysis, they attempted to account for
phylogenetic non-independence by assuming a Brownian motion model of
trait evolution. The revised estimates for effect sizes were largely
consistent with our own, and all remained significant except when
accounting for phylogenetic non-independence (Fig. 1). However, applying
this analysis to our data is problematic for three critical reasons.
First, the phylogenetic non-independence assumes that traits diverge
over time from the ancestral trait of a common ancestor (Felsenstein
1985). This assumption is violated by our data, as most traits are
non-homologous (Fig. S1). Second, the Brownian motion model assumes a
constant rate of evolution, but this assumption is often unrealistic for
traits under selection (Felsenstein 1985). Third, to analyze the data
with plants and animals, the Brownian motion model causes great loss of
statistic power due to the high variance-covariance estimated (Fig. S2
and S3). If we use other models of trait evolution, such as assuming an
accelerating rate of evolution (Blomberg et al . 2003) or assuming
incomplete phylogenetic dependence of trait evolution (Pagel 1997),
significant results are retained (Fig. 1). Importantly, whether the
results are significant or not depends on different assumptions of
evolutionary models rather than the data, and notwithstanding the
effects of different assumed evolutionary models, the effect size
remains consistent across models (Fig. 1). Thus, our main finding still
stands that transgenerational effects do indeed seem to be adaptive.
Concerning the transparency of our study and suggestions that the
peer-review was ineffective, both the data and R scripts of this study
have been provided since the first submission. Given this level of
transparency, the reviewers have already commented on most issues raised
by Sánchez-Tójar et al ., and we have responded accordingly. These
issues include searching in subject areas, dealing with missing
keywords, combining data from full-factorial and non-full-factorial
experimental designs, and further issues in the supplementary materials.
The reviewers also provided constructive suggestions for dealing with
difficult issues such as how to decide if a trait is negatively related
to fitness. To give even more transparency, a point-by-point reply to
reviewers from our initial study submission is provided as supplementary
material.
Finally, we agree with Sánchez-Tójar et al . that studies may have
been left out of our original meta-analysis. Indeed, transgenerational
effects are found across the tree of life, indicating that they either
have a deep evolutionary origin or have arisen many times (Salinaet al . 2013; Uller et al . 2013). An essential aim of our
meta-analysis was to reveal the specific scenarios that give rise to
transgenerational effects. Thus, we fully agree that meta-analyses
incorporating more data will further our understanding of when and where
transgenerational effects are adaptive.
We thank Sánchez-Tójar et al. for their comment, and we hope
these discussions will promote open science practice and inspire future
comprehensive meta-analyses of transgenerational effects.