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. 2024 Oct 2:4:1441373.
doi: 10.3389/fbinf.2024.1441373. eCollection 2024.

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

Júlio C M Chaves  1   2 , Fábio Hepp  2   3 , Carlos G Schrago  1 , Beatriz Mello  1
Affiliations

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

Júlio C M Chaves et al. Front Bioinform. .

Abstract

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification. Aiming to fill this gap, we inferred the phylogenetic relationships and divergence times for Holoadeninae using molecular data and calibration information derived from the fossil record of Neobatrachia. Our inferred phylogeny confirmed most genus-level associations, and molecular dating analysis placed the origin of Holoadeninae in the Eocene, with subsequent splits also occurring during this period. The climatic and geological events that occurred during the Oligocene-Miocene transition were crucial to the dynamic biogeographical history of the subfamily. However, the wide highest posterior density intervals in our divergence time estimates are primarily attributed to the absence of Holoadeninae fossil information and, secondarily, to the limited number of sampled nucleotide sites.

Keywords: Anura; MCMCTree; Neobatrachia; divergence times; timetree.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

FIGURE 1
FIGURE 1
Holoadeninae Timetree estimated in MCMCTree using a correlated rates model and four fossil calibration points (calibration scenario 1). Calibrated nodes are indicated with a dark-filled circle (calibration I is not shown because it corresponds to the divergence of the outgroup species, Rana temporaria, which was removed from the figure). The numbers inside the circles correspond to the calibration numbers defined in the methods section. Filled red circles indicate nodes that had Q1 support values from ASTRAL ≥0.75. Divergence time estimates are shown in black to the left of each node.
FIGURE 2
FIGURE 2
Comparison of RelTime relative time estimates (without using calibrations, x-axis) and MCMCTree absolute time estimates (using Calibration Scenario 1, y-axis). MCMCTree estimates using a correlated rate evolution model are represented by black dots, while estimates using an uncorrelated rates model are depicted by gray triangles. The dashed lines indicate the linear regressions through the origin, considering correlated rates (black, R2 = 0.99) and uncorrelated rates (gray, R2 = 0.97).
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Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. BM is supported by Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) (grants E-26/211.248/2019 and E-26/201.446/2022) and by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant 311231/2022-5). FH is supported by FAPERJ (grant E-26/210.312/2021). CGS is supported by CNPq (grants 409963/2023-2, 401725/2022-7, and 309165/2019-9). JCMC was supported by scholarship from CNPq (131863/2022-3).

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