Molecular clocks are essential for estimating the timing of evolutionary events, as they depend on precise calibration points to yield reliable divergence estimates. In previous studies, biogeographic events were used to calibrate molecular clocks for three Peracarida families (_Metacrangonyx_, _Pseudoniphargus_, and _Hyallela_), resulting in estimated divergence times for their most recent common ancestor (MRCA). However, when these three lineages are combined in a single phylogeny under an uncorrelated log-normal clock and calibrated with two isopod fossils, significant discrepancies in the divergence times emerged. This raises a critical question: What is the source of this inconsistency? (1) Are the biogeographic calibrations from the previous studies flawed, or (2) is the molecular clock model applied inappropriately for this dataset? This study aims to accurately estimate the true divergence times by identifying the most suitable molecular clock model. Specifically, we investigate two novel mixed clock models: (1) the Shrinkage-based Random Local Clock and (2) the Mixed Effects Clock. This study focuses on determining whether these models can resolve the incongruence between biogeographic and fossil-based calibrations, offering a more accurate understanding of Peracarida's evolutionary history.
Molecular clocks are essential for estimating the timing of evolutionary events, as they depend on precise calibration points to yield reliable divergence estimates. In previous studies, biogeographic events were used to calibrate molecular clocks for three Peracarida families (_Metacrangonyx_, _Pseudoniphargus_, and _Hyallela_), resulting in estimated divergence times for their most recent common ancestor (MRCA). However, when these three lineages are combined in a single phylogeny under an uncorrelated log-normal clock and calibrated with two isopod fossils, significant discrepancies in the divergence times emerged. This raises a critical question: What is the source of this inconsistency? (1) Are the biogeographic calibrations from the previous studies flawed, or (2) is the molecular clock model applied inappropriately for this dataset? This study aims to accurately estimate the true divergence times by identifying the most suitable molecular clock model. Specifically, we investigate two novel mixed clock models: (1) the Shrinkage-based Random Local Clock and (2) the Mixed Effects Clock. This study focuses on determining whether these models can resolve the incongruence between biogeographic and fossil-based calibrations, offering a more accurate understanding of Peracarida's evolutionary history.
TICK-TOCK, TUNE THE CLOCK: ONGOING SEARCH FOR PERACARIDA'S EVOLUTIONARY TIMELINE
ZANOLI, CHIARA
2023/2024
Abstract
Molecular clocks are essential for estimating the timing of evolutionary events, as they depend on precise calibration points to yield reliable divergence estimates. In previous studies, biogeographic events were used to calibrate molecular clocks for three Peracarida families (_Metacrangonyx_, _Pseudoniphargus_, and _Hyallela_), resulting in estimated divergence times for their most recent common ancestor (MRCA). However, when these three lineages are combined in a single phylogeny under an uncorrelated log-normal clock and calibrated with two isopod fossils, significant discrepancies in the divergence times emerged. This raises a critical question: What is the source of this inconsistency? (1) Are the biogeographic calibrations from the previous studies flawed, or (2) is the molecular clock model applied inappropriately for this dataset? This study aims to accurately estimate the true divergence times by identifying the most suitable molecular clock model. Specifically, we investigate two novel mixed clock models: (1) the Shrinkage-based Random Local Clock and (2) the Mixed Effects Clock. This study focuses on determining whether these models can resolve the incongruence between biogeographic and fossil-based calibrations, offering a more accurate understanding of Peracarida's evolutionary history.File | Dimensione | Formato | |
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https://hdl.handle.net/20.500.12608/77504