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Most paleogeographic maps available (C. R. Scotese or R. Blakey maps for instance) show not only the shape of the continents during the concerned period but also the level of the seas and oceans (i. e. the coastlines, the epicontinental seas, etc.).

Since Haq et al. 1987, there has been quite a few reconstructions of the global relative sea level changes for parts of the Phanerozoic. But going from such global curves to actual maps showing the approximative coastlines and epicontinental seas does require a fair amount of extra information such as paleobathymetry of the oceans and paleoaltimetry of the continents to name the more obvious.

So my question is: do we have such informations on a global scale? Or are the sea level representation on such maps just a shot in the dark?

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There are various plate tectonic models around, that are able to provide insight in paleobathymetry and -altimetry. These models include information on sea floor spreading and subduction, which provides much information on bathymetry. Also plate tectonic movement largely drives the uplift of mountain ranges, and combining this with isostatic effects of sediment loading, glaciation, etc. you can get a fair picture of paleoaltimetry as well. Of course this method provides only relatively low resolution data, and to get more detailed maps you need more localised data.

Outcrops and bore holes provide much information on the depositional environment, and for example sequence stratigraphy is a tool that can be used to predict/retrodict regional environments. If you know from a number of locations where the coastline was relative to its current position, and know from models etc. where the sampling locations were in the past you can map paleocoastlines as well.

So to answer your question shortly, yes there is a lot of global information available by combining large scale models and local investigations, and where such information is missing you can at least provide an educated guess of coastal positions.

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