Total evidence tip-dating phylogeny of platyrrhine primates and 27 well-justified fossil calibrations for primate divergences

Abstract

Phylogenies with estimates of divergence times are essential for investigating many evolutionary questions. In principle, “tip-dating” is arguably the most appropriate approach, with fossil and extant taxa analyzed together in a single analysis, and topology and divergence times estimated simultaneously. However, “node-dating” (as used in many molecular clock analyses), in which fossil evidence is used to calibrate the age of particular nodes a priori, will probably remain the dominant approach, due to various issues with analyzing morphological and molecular data together. Tip-dating may nevertheless play a key role in robustly identifying fossil taxa that can be used to inform node-dating calibrations. Here, we present tip-dating analyses of platyrrhine primates (so-called “New World monkeys”) based on a total evidence dataset of 418 morphological characters and 10.2 kb of DNA sequence data from 17 nuclear genes, combined from previous studies. The resultant analyses support a late Oligocene or early Miocene age for crown Platyrrhini (composite age estimate: 20.7-28.2 Ma). Other key findings include placement of the early Miocene putative cebid Panamacebus outside crown Platyrrhini, equivocal support for Proteropithecia being a pitheciine, and support for a clade comprising three subfossil platyrrhines from the Caribbean (Xenothrix, Antillothrix and Paralouatta), related to Callicebinae. Based on these results and the available literature, we provide a list of 27 well-justified node calibrations for primate divergences, following best practices: 17 within Haplorhini, five within Strepsirrhini, one for crown Primates, and four for deeper divergences within Euarchontoglires. In each case, we provide a hard minimum bound, and for 23 of these we also provide a soft maximum bound and a suggested prior distribution. For each calibrated node, we provide the age of the oldest fossil of each daughter lineage that descends from it, which allows use of the “CladeAge” method for specifying priors on node ages.

Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

“…A number of new Palaeogene and earliest Neogene South American fossil primates have been recovered outside of Platyrrhini and along the anthropoid stem in recent years [34,37,64], but the phylogenetic status of these taxa is highly uncertain owing to the very limited fossil material, typically a single tooth, and the preliminary nature of some analyses. Indeed, a recent tip-dating analysis [29] recovered the Early Miocene primate Parvimico as the sister to all other platyrrhines, rather than as the sister to crown anthropoids. We recommend that macroevolutionary researchers think carefully about whether to include fossils of such uncertain status in comparative phylogenetic analyses.…”

“…Biogeographic analyses based on molecular phylogeny [23] have suggested an Asian origin for crown group Primates, as well as crown clades such as Strepsirrhini (lemurs and lorises), Catarrhini (Old World Monkeys and apes) and Anthropoidea (South and Central American monkeys and the catarrhines). However, the first primates appeared near-simultaneously in Europe, Asia and North America [24][25][26][27][28][29] and palaeontological evidence indicates that their geographical distribution has varied substantially over time (electronic supplementary material, figure S1). Correspondingly, estimates of where major clades of primates originated and how they came to occupy their current geographical distributions differ substantially between studies based on extant taxa alone and those that consider information from the fossil record.…”

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

“…Instead of setting an a priori substitution model for each partition, we used the bModelTest module (Bouckaert & Drummond, 2017) within beast 2 to select the best model during the beast mcmc run. We set the tree prior to the Coalescent Bayesian Skyline model and added MRCA priors on the ages of 10 nodes based on well‐justified fossil calibrations (de Vries & Beck, 2021). Fossil calibration ages and distributions were based on de Vries and Beck (2021); specifically, we used a uniform distribution to constrain the timing of the divergences between Alouattinae and Atelinae (13.363–34.5 Ma), Callicebinae and Pitheciinae (13.032–34.5 Ma), Callitrichidae and Cebidae (13.183–34.5 mya), Cebinae and Saimiri (13.032–34.5 Ma), Platyrrhini and Catarrhini (33.4–56.035 Ma), Cercopithecoidea and Hominoidea (25.193–33.4 Ma) and tarsiers and anthropoids (41–66.095 Ma).…”

“…We set the tree prior to the Coalescent Bayesian Skyline model and added MRCA priors on the ages of 10 nodes based on well‐justified fossil calibrations (de Vries & Beck, 2021). Fossil calibration ages and distributions were based on de Vries and Beck (2021); specifically, we used a uniform distribution to constrain the timing of the divergences between Alouattinae and Atelinae (13.363–34.5 Ma), Callicebinae and Pitheciinae (13.032–34.5 Ma), Callitrichidae and Cebidae (13.183–34.5 mya), Cebinae and Saimiri (13.032–34.5 Ma), Platyrrhini and Catarrhini (33.4–56.035 Ma), Cercopithecoidea and Hominoidea (25.193–33.4 Ma) and tarsiers and anthropoids (41–66.095 Ma). Divergences between Cercopithecini and Colobini (12.47–25.2 Ma), Hominoidea and Hylobatidae (13.4–25.2 Ma), and Haplorhini and Strepsirrhini (55.935–66.1 Ma) were constrained with exponential distributions, where the minimum age was used as the offset and the mean was set to place the maximum age at the 95% quantile.…”

The Complete Mitochondrial Genome of Dendrogale murina (Tupaiidae) and Phylogeny of Scandentia

“…Three fossil calibration points were applied to constrain the analysis. The total tree height (node A) was considered a log-normal prior (with the offset = 65.79 MYA and 95 % HPD of 126-67 MYA), as was done in Vries and Beck [ 38 ], according to the fossil Purgatorius mckeeveri Wilson Mantilla et al, 2021, from the early Palaeocene [ 39 ]. The most recent common ancestor (MRCA) of Scandentia representatives (node B) was calibrated with a log-normal distribution (with the offset = 34 MYA and 95 % HPD of 65-34 MYA), based on the fossil of P. kylin from the early Oligocene [ 13 ].…”