I go with Ice Core examples since early sociteties probably didn't have Written Records or maps, and tree rings would only tell if they were fossilized. I hope this helped :)
Answer:
By eating things with protein in it. Sorry if this sounds too simple, but that's all it is.
By using microscopes scientists were able to discover the existence of microorganisms, study the structure of cells, and see the smallest parts of plants, animals, and fungi.
George Monbiot is spearheading the Rewilding Movement. The environmentalist and writer is prominent in the platform. He was featured in TED Talk and talked about a large scale conservation approach aiming to restore the lost habitats. Here is an excerpt of his speech where he discusses the lost megafuna:
"What megafauna, you say? Well, every continent had one, apart from Antarctica. When Trafalgar Square in London was excavated, the river gravels there were found to be stuffed with the bones of hippopotamus, rhinos, elephants, hyenas, lions. Yes, ladies and gentlemen, there were lions in Trafalgar Square long before Nelson's Column was built. All these species lived here in the last interglacial period, when temperatures were pretty similar to our own. It's not climate, largely, which has got rid of the world's megafaunas. It's pressure from the human population hunting and destroying their habitats which has done so."