Substantial variation in species ages among vertebrate clades

Abstract

Ecological and evolutionary studies traditionally assume that species are comparable units of biodiversity. However, not only this assumption is rarely tested, but also there have been few attempts even to assess variation in most emergent, species-level traits and their corresponding underlying mechanisms. One such trait is species age, here defined as the time since the most recent common ancestor between a given species and its sister lineage. In this study, we demonstrate that different terrestrial vertebrate clades vary considerably in the age of their constituent species. In particular, species ages were youngest in mammals and birds as opposed to squamates and amphibians, although considerable variation was found within those clades as well. Sensitivity analyses showed that these results are unaffected by phylogenetic uncertainty or incomplete taxonomic sampling. Interestingly, there was little geographical correspondence in mean species age across taxa, as well as with temperature and precipitation stability over the past 21,000 years. We discuss candidate mechanisms that might explain differences in species ages among clades, and explore the implications of these findings in relation to recent advances in age-dependent speciation and extinction models of diversification.

Challenges in estimating species age from phylogenetic trees

“…For example, Sonne et al (2022) determined young and old Andean hummingbirds by assessing the sensitivity of their results to incomplete taxon sampling by generating 1000 trees with randomly missing species. Pie & Caron (2023) accounted for taxonomic incompleteness by pruning an additional 1 -5% of species and evaluated if their conclusions changed and found that they did not. Yet, the magnitude of the error associated with the direct use of the length of phylogenetic branches as estimators of species ages remains under-appreciated, as shown by the many studies implementing this approach.…”

“…The use of branch lengths of phylogenetic trees as an approximation of species ages is becoming central to an increasing number of studies that use them to evaluate the relationship among macro-ecological and evolutionary patterns and current extinction risks (Pie & Caron, 2023;Sonne et al, 2022;Tanentzap et al, 2020;Verde Arregoitia et al, 2013).…”

“…The use of branch lengths of phylogenetic trees as an approximation of species ages is becoming central to an increasing number of studies that use them to evaluate the relationship with macroecological or evolutionary patterns, for instance current extinction risks (Pie & Caron, 2023; Sonne et al, 2022; Tanentzap et al, 2020; Verde Arregoitia et al, 2013). Here we showed that this approximation leads to substantial errors and that its accuracy is hampered by three shortfalls: incomplete sampling of extant species, unobserved extinction events, and unknown speciation mode.…”

“…Species ages estimated from paleobiological data offer a reliable measure of species’ temporal duration which can be used in macroevolutionary studies (Benton, 2016; Silvestro et al, 2020; Van Valen, 1973). More recently, several studies have used the length of terminal branches in time-calibrated phylogenies as a proxy for the age of extant species, an approximation that we hereafter refer to as “phylogenetic age” (Alzate et al, 2023; Davies et al, 2011; Gaston & Blackburn, 1997; Johnson et al, 2002; Pie & Caron, 2023; Sonne et al, 2022; Tanentzap et al, 2020; Verde Arregoitia et al, 2013). These phylogenetic ages have been used as the basis to test for links between species age and current extinction risks (Tanentzap et al, 2020; Verde Arregoitia et al, 2013) and to assess various correlations with evolutionary, biogeographical, and ecological patterns in living species (Alzate et al, 2023; Freer et al, 2022; Kennedy et al, 2022; Pie & Caron, 2023)…”

“…More recently, several studies have used the length of terminal branches in time-calibrated phylogenies as a proxy for the age of extant species, an approximation that we hereafter refer to as "phylogenetic age" (Alzate et al, 2023;Davies et al, 2011;Gaston & Blackburn, 1997;Johnson et al, 2002;Pie & Caron, 2023;Sonne et al, 2022;Tanentzap et al, 2020;Verde Arregoitia et al, 2013). These phylogenetic ages have been used as the basis to test for links between species age and current extinction risks (Tanentzap et al, 2020;Verde Arregoitia et al, 2013) and to assess various correlations with evolutionary, biogeographical, and ecological patterns in living species (Alzate et al, 2023;Freer et al, 2022;Kennedy et al, 2022;Pie & Caron, 2023) While several studies have used phylogenetic age at face value for species age (e.g., Johnson et al 2002;Tanentzap et al 2020;Verde Arregoitia et al 2013), their potential deviation from the true species ages remains unclear. Specifically, we identify three nonmutually exclusive shortfalls that can lead to over-or underestimation of species ages.…”