Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Abstract

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

High diversity of pimpline parasitoid wasps (Hymenoptera, Ichneumonidae, Pimplinae) from the lowermost Eocene Fur Formation

“…The diversity within Pimplinae appears skewed towards particular genera and body shapes when compared to extant communities. A recent study using total-evidence dating to calibrate the phylogeny of Pimpliformes (Spasojevic et al 2021) indicates that all the pimpline tribes started radiating already deep in the Cretaceous, suggesting that another explanation than age is needed to resolve this discrepancy. This remains true even when considering that Pimplinae as the subfamily is currently understood is probably paraphyletic (Klopfstein et al 2019a).…”

“…For instance, some genera currently classified in the extinct Labenopimplinae, such as Rugopimpla Kopylov, might well represent stem representatives of extant subfamilies (D. Kopylov, personal communication). Second, a recent molecular study (Spasojevic et al 2021) has estimated the age of the radiation of the nine subfamilies that form the clade called Pimpliformes to the Middle Jurassic period, implying the appearance of most extant subfamilies deep in the Mesozoic. Even though such an old age estimate for Pimpliformes is at odds with the oldest known fossil attributed to this group, which stems from the late Paleocene (Piton 1940), the size of the gaps in the described fossil record of Darwin wasps implies that it is far from unlikely.…”

New fossil wasp species from the earliest Eocene Fur Formation has its closest relatives in late Eocene ambers (Hymenoptera, Ichneumonidae, Pherhombinae)

“…Of the 222 characters coded in the morphological matrix by Spasojevic et al (2021), we excluded 12 characters that either became uninformative under our restricted taxon sampling or consisted of large amounts of missing data and could in any case not be coded [Table 1 around here] We added two characters that are informative about Mesochorinae and Pherhombinae: "Flagellomere 1: ratio of length to width" (continuous); and "Forewing vein 1-M+1-Rs: length compared to length of r-rs" (continuous). In another two cases, we added states to existing characters in order to account for the newly included taxa: #133 ("Distal abscissa of Rs (4-Rs): shape"): (state 5) evenly arched towards 2-R1; #163 ("Tergite 1: shape from above"): (state 3) no clear separation of postpetiolus, constriction in the anterior half, thus expanding again towards the anterior margin.…”

Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process

“…The resolved FBD process often poorly resolves the phylogenetic positions of fossil taxa, even when the relationships among extant taxa are reconstructed with confidence (Zhang et al 2016;Luo et al 2020). This problem can perhaps be attributed to the use of poorly fitting models of morphological evolution (e.g., the typical Mk model; Lewis 2001;Goloboff et al 2019;Gavryushkina and Zhang 2020), uncertainty in fossil ages, and/or low informativeness of morphological characters (O'Reilly et al 2015;Luo et al 2020;Spasojevic et al 2021). Moreover, the extent of among-lineage rate heterogeneity and convergent evolution in morphological characters, as well as the typically high proportion of missing characters for many fossil specimens (Sansom and Wills 2013;Lee and Palci 2015; O'Reilly and Donoghue 2021), have negative impacts on estimates of evolutionary parameters.…”

“…Moreover, the extent of among-lineage rate heterogeneity and convergent evolution in morphological characters, as well as the typically high proportion of missing characters for many fossil specimens (Sansom and Wills 2013;Lee and Palci 2015; O'Reilly and Donoghue 2021), have negative impacts on estimates of evolutionary parameters. These problems could potentially contribute to overestimation of divergence times in practice (e.g., Wood et al 2013;O'Reilly et al 2015;Ronquist et al 2016;Spasojevic et al 2021).…”