The rate of extinction among amphibians is alarming – scientists estimate that that about 200 frog extinctions have occurred and that the next century will see the loss of hundreds more. That suggests an extinction rate for amphibians and reptiles at some 10,000 times larger than for all other organisms. Why is not clear – a variety of factors such as habitat destruction and disease could be playing a part. A new study in Kenya is using genomics – the branch of molecular biology concerned with genetics – to fill critical gaps in data and information on the extinction risks that amphibians face. This will help to fast track the development of effective conservation strategies.
Using new techniques to track Kenya’s disappearing amphibians
BY SHARON KAHARA | THE CONVERSATION | 7 SEPTEMBER 2017
Amphibians are cold-blooded vertebrates that live part of their life on land, part of it in water – a popular example are frogs. What isn’t widely known is that around the world they are going extinct at rates that far exceed other vertebrates.
A recent study showed how the number of vulnerable and endangered amphibians is nearly double that of birds or mammals. Approximately 1,000 mammals and 990 birds are classified as at risk, while over 1,800 amphibians face extinction.
Most amphibian losses are attributed to habitat destruction. This leads to reduced resources (such as food and cover), population decline and it also fragments populations, reducing genetic vigour. In some cases, over-exploitation, disease, non-native predators and climate change have alsobeen implicated.
An assessment of amphibians estimated that a fifth (235) of species in sub-Saharan Africa are threatened with extinction. Another 201 species lack enough information to make any conclusions about their status. This pace of amphibian loss warrants a quick effort to collect relevant information.
But amphibians are a challenge to research. At various stages of their lives, they live on both land and water. They also move around their environment in response to daily or seasonal changes in temperature and moisture. This means that classical biodiversity assessment approaches can be labour intensive and time consuming.
Methods like visual encounter survey (VES), for example, involve slowly walking through amphibian habitat searching for expertly camouflaged individuals. It takes years of practice to avoid misidentification, spooking or harming individuals. Another effective method, for accurate species, sex and age determination, involves trapping and capture. But this can be costly in terms of equipment, time and labour.
In Africa these challenges have resulted in a limited number of selective, sporadic studies spread over several decades.
The first major goal of our project is to collate information about amphibians in Kenya. This will be built from existing records, mainly from the vast Museum specimen collection, and will enable us to create a digital inventory with room for updates. The inventory will be used to develop predictive occurrence maps that determine historic distributions, prior to human habitat alteration, and show how these may have changed under present conditions.
Our second goal will be to develop a genetic library or DNA “barcode” of amphibian species in Kenya with the aim of eventually expanding to the continent at large.
There is a rapid rise in the use of genomics – the branch of molecular biology concerned with genetics – as a standard ecological assessment technique. This allows us to trace organisms in their natural habitats and may help hasten research progress and outcomes. These techniques are relatively less intrusive than traditional surveys and potentially more accurate.
We will be using next generation sequencing (NGS) of DNA, a method used to determine the exact order in which the basic building blocks of life are arranged. NGS is more expansive and a faster way to map the DNA of great numbers of amphibians before populations disappear in rapidly changing environments. It allows us to genetically archive species and establish the exact classification (taxonomy) of specimens that have not been studied since their initial description.
A third, and key, goal of our project will be to use the DNA barcodes to identify patterns of occurrence at the landscape scale using environmental DNA (eDNA) techniques. This will involve detection of species from environmental samples in which DNA can persist, such as soil, sediments or water. This offers opportunities to better understand dispersal patterns and genetic relatedness among meta-populations.
Surprisingly, this technique has not had much use in Africa. Yet its applicability may enhance our ability to detect rare or invasive species in isolated or difficult to access habitats.
Once the information has been gathered, there is still an immense challenge in trying to conserve amphibians.
Habitat destruction is a huge factor in their decline. But conserving their habitat is made even harder due to their complex life cycles, which are dependent on both land and water. For example, adult frogs can move over 2km away from their natal pond in the non-breeding season, spending months in upland forests or even buried underground. They then migrate to water in the breeding season to mate.
Unlike reptilian or bird eggs that have a protective outer layer, frog eggs are enclosed in a gelatinous envelope. Eggs then hatch into tadpoles, an aquatic stage that is completely dependent on water to survive and grow.
Aquatic ecosystems are therefore key to the success of amphibian populations but, unfortunately, worldwide freshwater systems are being degraded.
In Kenya, for instance, rapid human population growth, expanding urban and agricultural areas, poor infrastructure and unregulatedindustrial and residential waste pose major threats to rivers, lakes and wetlands.
This is expected to lower ecosystem resilience and biodiversity while increasing the prevalence of water borne diseases and parasites. This will result in the decline and extinction of aquatic species across the globe.
The problem is that fixing the causes of the degradation is also a huge challenge. In urban areas, for example, a lack of basic services – such as solid waste removal and sewage treatment – often lead to freshwater pollution. Reversing these problems will involve heavy commitment from government as well as the communities affected.
It could be easier in the case of major polluters, such as urban developers, where government agencies could get involved. Tasked with environmental protection, they could enforce discharge restrictions and take a conservative approach to permit approval. These agencies should also develop strategies that adapt allowable discharge limits according to the impacts on sensitive species.
The goal of this project is to fill existing knowledge gaps on amphibians in Africa and ensure that the technology we use becomes self-sustaining and functional for generations to come. To achieve this, students will play a key role, forming the core of research activity through undergraduate and graduate research.
We will also expand our funding avenues to ensure that we don’t rely solely on external funding. Resources and researchers and must actively mobilise widespread local support from public and private sectors.