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Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

ABSTRACT: BACKGROUND: Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates. RESULTS: According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic. CONCLUSION: This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.

SUBMITTER: Hipsley CA

PROVIDER: S-EPMC2719621 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

Hipsley Christy A CA Himmelmann Lin L Metzler Dirk D Müller Johannes J

BMC evolutionary biology 20090701

<h4>Background</h4>Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenet ...[more]

PMID: 19570207

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Project description:While running, small animals frequently encounter large terrain variations relative to their body size, therefore, terrain variations impose important functional demands on small animals. Nonetheless, we have previously observed in lizards that running specialists can maintain a surprisingly good running performance on very uneven terrains. The relatively large terrain variations are offset by their capacity for leg adjustability that ensures a 'smooth ride' of the centre of mass (CoM). The question as to how the effect of an uneven terrain on running performance and locomotor costs differs between species exhibiting diverse body build and locomotor specializations remains. We hypothesise that specialized runners with long hind limbs can cross uneven terrain more efficiently than specialized climbers with a dorso-ventrally flattened body and equally short fore and hind limbs. This study reports 3D kinematics using high-speed videos (325?Hz) to investigate leg adjustability and CoM movements in two lacertid lizards (Acanthodactylus boskianus, running specialist; Podarcis muralis, climbing specialist). We investigated these parameters while the animals were running on a level surface and over a custom-made uneven terrain. We analysed the CoM dynamics, we evaluated the fluctuations of the positive and negative mechanical energy, and we estimated the overall cost of transport. Firstly, the results reveal that the climbers ran at lower speeds on flat level terrain but had the same cost of transport as the runners. Secondly, contrary to the running specialists, the speed was lower and the energy expenditure higher in the climbing specialists while running on uneven terrain. While leg movements adjust to the substrates' variations and enhance the stability of the CoM in the running specialist, this is not the case in the climbing specialist. Although their legs are kept more extended, the amplitude of movement does not change, resulting in an increase of the movement of the CoM and a decrease in locomotor efficiency. These results are discussed in light of the respective (micro-)habitat of these species and suggest that energy economy can also be an important factor for small vertebrates.

Project description:BACKGROUND: Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively derived in their morphology (e.g. Brachyrhinodon), an earlier unknown history of Lepidosauria is implied. However, molecular age estimates for Lepidosauria have been problematic; dates for the most recent common ancestor of all lepidosaurs range between approximately 226 and 289 Mya whereas estimates for crown-group Squamata (lizards and snakes) vary more dramatically: 179 to 294 Mya. This uncertainty restricts inferences regarding the patterns of diversification and evolution of Lepidosauria as a whole. RESULTS: Here we report on a rhynchocephalian fossil from the Middle Triassic of Germany (Vellberg) that represents the oldest known record of a lepidosaur from anywhere in the world. Reliably dated to 238-240 Mya, this material is about 12 million years older than previously known lepidosaur records and is older than some but not all molecular clock estimates for the origin of lepidosaurs. Using RAG1 sequence data from 76 extant taxa and the new fossil specimens two of several calibrations, we estimate that the most recent common ancestor of Lepidosauria lived at least 242 Mya (238-249.5), and crown-group Squamata originated around 193 Mya (176-213). CONCLUSION: A Early/Middle Triassic date for the origin of Lepidosauria disagrees with previous estimates deep within the Permian and suggests the group evolved as part of the faunal recovery after the end-Permain mass extinction as the climate became more humid. Our origin time for crown-group Squamata coincides with shifts towards warmer climates and dramatic changes in fauna and flora. Most major subclades within Squamata originated in the Cretaceous postdating major continental fragmentation. The Vellberg fossil locality is expected to become an important resource for providing a more balanced picture of the Triassic and for bridging gaps in the fossil record of several other major vertebrate groups.

Dataset Information

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

Publications

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards.

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