The Japanese giant salamander (JGS, Andrias japonicus) is a large, aquatic salamander with a flattened body shape and multiple folds of skin along its sides. The head is also wide and flat, with small eyes on each side. Their limbs are short and stout, having four fingers and five toes that are not webbed. Their tails are large, sometimes over half of their body's length. Their coloration varies a lot, but are generally a reddish-brown to purple in adults, with a paler belly marked with many spots. Younger ones are usually lighter in color, sometimes closer to yellow with darker spots.

There is little difference between males and females until the breeding season comes when mature males will have a swollen cloaca and the females are noticeably larger while holding their eggs. Young JGS are similarly colored and have large, external gills which disappear as they grow.

The Chinese giant salamander is very similar in appearance but has tubercles (warty outgrowths) arranged in two rows on the head and neck, whereas with the JGS they are larger and scattered in the same area. The JGS also has a more rounded snout and shorter tail. These differences are difficult to distinguish, even for a trained eye, leaving DNA analysis the best option to tell which species an individual is.

The JGS is a fully aquatic and nocturnal creature, seldom seen out of water or during the daytime. Outside of the breeding season, they tend to stay in small sections of a river, hunting at night and limiting actions during the day. While they can disperse over long distances, once a favored and unoccupied habitat is found they tend to stay put. Depending on the population density and available habitat, there can be some territorial interactions with other JGS, but this activity greatly increases in the breeding season.

Late summer is when the JGS becomes much more active, sometimes travelling long distances to find the best breeding site. Competition between males is fierce, where it is not uncommon to find dead and heavily injured males. Generally, the largest males will control the most suitable sites and are called “den-masters”. If these sites are suitable enough, they can be used by the same individuals year after year. These den-masters will also patrol the surrounding area to keep other males away. Eventually, females come by and enter the den-site to lay eggs, which are externally fertilized. Sometimes, smaller, opportunistic males see this as a chance, trying to intrude and fertilize the eggs themselves. Regardless of the outcome, the den-master stays heavily committed to the eggs now in his nest.

The eggs are then aggressively guarded and protected until they hatch in early autumn.  Males not only protect the eggs, but also exhibit high quality brooding behaviors.  By fanning their tail, they circulate the water over the clutch of eggs, keeping it clean and well oxygenated.  They will also find and remove dead, unfertilized or infected eggs, avoiding further complications . Once hatched, the larvae disperse on their own, generally hiding well into the river's gravel bed away from potential predators.  They take a long time to grow out of the larval stage, up to 5 years. Once they do, they disperse to the surrounding waterways to stake claim to their own piece of the river.

JGS are indeed able to regrow bone. However, in adults the regrowth is inferior to the original. For example, a leg might regrow as a stump which is beneficial for walking, as the toes have some level of dexterity, but is not as good as the original.

Expanding development projects and constructed river barriers such as weirs and dams have restricted the salamanders’ ability to move and breed.

Because these barriers inhibit the free movements of salamanders across their native rivers, identifying the most intrusive locations of weirs is imperative for creating a sustainable conservation plan and ensuring salamanders’ survival.

Chinese giant salamanders (CGS) are thought to have been originally brought to Japan as a supplementary food source. Since then, individuals have entered into wild JGS populations and began creating hybridized offspring in Mie, Kyoto, Nara and Okayama prefectures. Hybridization of the two species adds unknown variables into the challenges of JGS conservation. Hybrid offspring have the potential for lower fitness which can then spread into native JGS populations. On the other hand, hybrids could gain an advantage and begin to outcompete native JGS populations, even to the extent of extirpation. With the outcomes being almost impossible to predict, it in turn makes it increasingly complicated to form well constructed conservation plans for the native JGS population. At present, the current practice is the removal of CGS and hybrids from JGS habitats if such individuals are identified.

Amphibians such as the Japanese giant salamander (JGS) breathe through their thin, porous skin, directly absorbing oxygen from the water in their environment. Many also spend most of the early stages of their life cycle growing and developing in the water as eggs and then juvenile larva. In order for them to absorb enough oxygen and develop normally through their life cycle, the water quality of their habitat is crucial. Key factors are the dissolved oxygen (DO) levels, turbidity (cloudiness of the water), and absence of chemical pollutants. Ideal conditions are cool flowing waters which can hold higher levels of DO with low turbidity, or low levels of floating organic matter or sediment which can smother eggs or larva and support bacterial growth that reduces DO. Human development in salamander habitat has reduced the water quality by altering water flow through the placement of weirs and increasing sediment deposition through road construction. Additionally, chemicals from agricultural runoff may also be seeping into the waterways which can result in reduced survival and slowed growth of offspring. In order for healthy salamander populations to persist, healthy water quality conditions will need to be restored.

Amphibians, like frogs, salamanders, and newts, live in wet environments and often spend part or all of their life in or near water. Many species will lay their eggs in the water and spend their larval stages (tadpoles, juveniles) growing in the water. Once they become full adults, they may continue to live mostly in or near water. This is because unlike reptiles, which have dry scaly skin to protect them from the elements, amphibians have thin, moist skin that they use to absorb oxygen directly from the water in their environment. This is called cutaneous respiration, or breathing via their skin.

Just below the surface of their thin, porous skin are networks of blood capillaries. Having capillaries near the surface of their skin makes it easier to absorb oxygen, as there is a shorter distance for it to travel from the water in their environment, through their skin, and into their bloodstream. It varies among different species, but some may get most of the oxygen their body needs through their skin. Some species, such as the Hellbender salamander and JGS, even have extra folds in their skin to increase the surface area to absorb oxygen. Species that get most of their oxygen through their skin may have reduced lungs that are used for controlling their buoyancy in the water instead of breathing, like the Japanese giant salamander.

For animals that spend a large portion of their life in the water, and absorb most of their oxygen through contact with it, water quality is of great importance. Water with higher dissolved oxygen (DO) levels will be easier for amphibians to live in. In fact, studies show that aquatic habitats with higher levels of DO support more amphibians. The level of dissolved oxygen in the water is related to factors such as water temperature and turbidity, or the amount of sediment or organic matter floating in the water.

Temperature

Cold water can hold more dissolved oxygen, and flowing water tends to have more DO than stagnant or still water. Fast flowing rivers and streams, where the water is churned up as it flows down in elevation or across rocks, are going to naturally be a cooler temperature and have more dissolved oxygen due to the constant movement of water. The sources that feed these bodies of water, such as snowmelt, can also contribute to the lower base temperature.

In contrast, warm or stagnant water will hold less DO and be more difficult for some organisms to absorb enough oxygen. Shallow or disconnected bodies of water, such as ponds or drainage culverts, will have less water movement and more time to absorb heat throughout the day, resulting in less dissolved oxygen. 

Turbidity

The amount of organic matter or sediment floating in the water, turbidity, also plays a role in oxygen availability. A high level of organic matter coupled with warm temperatures can result in the growth of bacteria which absorbs the oxygen in the water and decreases the DO levels. Additionally, sediment deposits on the bottom of the waterway can essentially smooth it out, reducing natural aeration that would occur as the water flows across the rocky bottom and further reducing DO levels.

High levels of sediment, such as sand and soil, can also affect the eggs and larvae of amphibians which can become smothered as it settles over them or builds up on the rocky surfaces they would usually hide in or find their prey. In fact, increased sedimentation can cause negative impacts throughout the food chain as turbid waters let less light through for plants and phytoplankton, reducing primary food sources for smaller organisms like invertebrates which would normally feed small amphibians and fish. These effects in turn, mean less food for larger vertebrates like larger fish and amphibians such as the Japanese Giant Salamander.

Human agriculture and development have direct effects on water quality by changing the flow, temperature, and turbidity of the water. The construction of dams or roads disrupt the natural flow of the water and introduce more sediment into the waterways. 

When obstacles that block the natural flow of water, such as dams or weirs, are put into place they alter the flow of the river by increasing the water levels upstream and reducing water levels downstream. Behind these structures where the water pools, it tends to slow the flow of the water. When the water slows down, it results in more sediment being deposited behind and around the obstacle and higher water temperatures as the slow speed allows more time for the water to absorb ambient heat throughout the day. Downstream, water temperatures can also increase because shallow water heats up more quickly, reducing DO levels along the length of the waterway and increasing turbidity in impacted sections.

Additionally, construction of other nearby structures such as roadways can result in even more sediment entering the waterway and depositing in slow moving areas. As stated above, this increase in turbidity can affect early stages of the amphibian life cycle and reduce nesting areas as the buildup covers natural crevices and gaps that amphibians and their prey shelter in.

Agricultural practices also pose a problem as the widespread and sometimes heavy use of chemical pesticides used to protect crops and fertilizers to aid growth leads to an influx of chemicals into natural waterways, creating additional problems for amphibian survival and reproduction.

As chemical fertilizers and pesticides are washed down into natural waterways, they have several negative effects on amphibian populations (and other aquatic wildlife). An increase in nutrients, especially nitrogen, from fertilizers can spur the growth of algae. In water that has become warm, slow or stagnant this supports increased algal growth which further reduces the DO levels. As discussed earlier, lower oxygen levels means it is more difficult for aquatic life to breathe. 

Studies show that higher levels of chemical pollutants, such as pesticides, reduce the reproductive fitness of amphibians. Spending most of their early life stages as fully aquatic organisms, constant exposure and absorption of aquatic pollutants through their egg membranes or thin skin during larval and juvenile stages results in reduced egg survival and slower growth and development. Even before this stage, higher chemical levels can cause fewer eggs to be laid in the first place. (Egea-Serrano et. al., 2012)

Together, these represent challenges to amphibian populations' ability to sustain or grow their numbers as reproduction is affected at multiple levels. 

Japanese giant salamanders thrive in cool, flowing waters at higher elevations but in the Mt. Daisen area they are present in higher than usual numbers for a lower elevation, due to the historical conditions of the Nawa river basin. Fed by snowmelt and high rainfall, the rivers and streams in the basin are filled with cool flowing waters. Historically treated as sacred and left untouched, the basin’s waters were once nutrient and oxygen rich in their entirety, from source to ocean. However, increased development of roads and weirs has led to fragmentation and blockage of their waterways.

Large-bodied animals such as the Japanese giant salamanders require a lot of oxygen, so maintaining sufficient levels of dissolved oxygen is necessary for their survival from the egg to adult stages. This is reflected in their behavior, as adult males will tend their eggs by fanning them with their tail to ensure they are adequately oxygenated. And, as stated above, clean water with low turbidity is essential for eggs and juvenile stages to survive and develop normally. 

In addition to water quality issues resulting from the weirs, their role as a physical barrier is of immediate concern. After heavy rainfall, the salamanders have been washed downstream over the weirs and unable to climb back up over the barrier to move back upstream. Due to ongoing effects of climate change, instances of heavy rain seem likely to occur more frequently and therefore instances of salamanders being washed downriver may increase as well. If individuals become concentrated downstream and prevented from moving back upstream to hunt or breed, it may become difficult for the population to sustain itself as more individuals compete over limited space and resources, and breeding behavior is disrupted. To ensure the survival of this unique species, impacts of weir and road construction will need to be addressed and adequate water quality restored and maintained.

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