The route through the museum starts with a display of various rocks and fossils that are found in river beds of the area.
Two million years ago the area was dominated by forests of Metasequoia. The fossil stump of a large Metasequoia tree displayed in the museum died approximately two million years ago after reaching an age of 400 years. It was only recently exposed by erosive floodwater of the Eichi River, east of Lake Biwa. With the fossilized stump, researchers also found elephant footprints and fossil insects and plants. This information has helped to build up an idea of life in the area two million years ago.
The rocks that underlie the lowlands and form the mountains of Shiga Prefecture consist of igneous, metamorphic and sedimentary types.
Igneous rocks, such as granite, formed by the slow solidification of molten rock deep in the crust. Later, these igneous rocks were uplifted and now form many of the mountains in the area. Basalts are solidified volcanic lava, and welded tuffs consist of volcanic material that was sufficiently hot at time of eruption to weld together. Sedimentary rocks, such as mudstones, limestones and sandstones, were formed by the compaction of sediments.
Twenty-five million years ago, the Sea of Japan did not yet exist, and the land destined to become Japan was still part of the eastern margin of continental Asia. Through the process of tectonic rifting, the eastern margin of the continent developed a large rift valley that contained one or more freshwater lakes. As the rifting continued, about 22 million years ago, saltwater began to flood the rift valley, and by 19 million years ago the rift had become a continuous saltwater strait, the beginning of the Sea of Japan.
Seventeen million years ago, the southeastern corner of Shiga Prefecture was covered by the sea. Fossil dolphins, whales, sharks, seals, fish, marine clams, oysters and snails have been found from this time and are on display in the museum.
East Asia is home to a huge number of freshwater fish of the Cyprinidae family (the carp family). Some of these fish evolved in the freshwater lakes that formed in the rift valley that was the beginning of the Sea of Japan. This long, narrow lake lasted several million years and was home to many of the ancestors of Lake Biwa's fish, including cyprinids.
The fossil teeth of these fish are very useful for studying their evolution.
Lake Biwa is a member of a very special group of lakes called ancient lakes. These lakes have an uninterrupted history of longer than 100 000 years, and there are fewer than 30 such lakes in the world. The Lake Biwa region has a lake history stretching back four million years, when Lake Oyamada formed to the southeast of the location of the present-day lake.
Such ancient lakes are biologically very interesting as they often contain endemic species (species that are found nowhere else) that have evolved in the lakes. The secret to their longevity is subsidence; if subsidence rates are faster than sediment can fill up the lake, they continue to survive and get deeper over time. The land below Lake Biwa has subsided 720m over the last 800 000 years and the lake will continue to get deeper.
Between 3.5 and 4 million years ago the climate of the region was subtropical. During that time, a small, shallow lake, Lake Oyamada, existed to the south east of the present Lake Biwa. Large mud snails, two-metre long carps and now extinct fish lived in the lake together with very large soft-shelled turtles and crocodiles. The shores of the lake were inhabited by the Mie elephant, which could reach a height of 4 m at the shoulder.
In total, five species of elephant have lived in the region over the last three million years, but their distribution ranges shifted as the climate became colder.
Two million years ago the area was dominated by the Gamo Lakelands, surrounded by a forest of 20- to 30- meters-high Metasequoia. Reduced mostly to swamplands, the Gamo Lakelands were still not at the present location of Lake Biwa. The climate had cooled slightly from two million years earlier, but was still warm. The Mie elephant had already disappeared and a smaller species, the Akebono elephant now lived here.
Later, about one million years ago, when the climate became even colder, the Akebono elephant also disappeared from Japan.
To find out what happened to the lake during the last million years, a 900m core was drilled below the present site of the aquarium in 1992.
Analysis of the core revealed that during the past 1.5 million years the site was located either near to the lake shore, or near a river which flowed into the lake. Among the sedimentary strata present in the core were deposits of volcanic ash that had settled out in the lake basin after volcanic eruptions elsewhere. These ash layers can be dated precisely, making it possible to trace the succession of events revealed by the different kinds of sediment in the core and their relation to the dated ash layers. The surface of the core corresponds to the present time, and the bottom to 1.8 million years ago.
Lake Biwa is home to many endemic species, i.e. species that live only in Lake Biwa and its connected rivers, and nowhere else in the world. About 54 fish species are native to this lake basin, and 13 (25%) of them are endemic at the species or subspecies level. Endemism reaches 39% for snails (Gastropoda) and 56% for mussels and clams (Bivalvia).
Well known examples of endemic fish are the Lake Biwa catfish, the Lake Biwa salmon and two kinds of crucian carps. Other species, like the lakeweed chub and some shellfish, are known as relict endemics. This means that in ancient times they were widely distributed, but now are found only in Lake Biwa.
The techniques used by researchers to reconstruct the history of Lake Biwa are very varied. Palaeontological sites, often in river beds, have been carefully examined and information on fossils, sediment type and age of the strata carefully collected.
Back in the laboratory, researchers first clean the fossils using drills, brushes and hammers and then identify them. For very small fossils, such as fossil fish teeth or ostracods, a scanning electron microscope may be used. Some of these techniques and tools are displayed in the Natural History Laboratory.
By the exit of the Natural History Laboratory is a model of a sediment profile from the future. Sedimentation in a continuous process: it happened in the past, it is occurring now, and it will continue in the future.