Although Amur tigers have smaller populations and less genetic diversity than Indian tigers, they are not isolated from each other. So they don’t suffer from inbreeding. Photo: Photo: s-brickman/Flickr, CC BY-SA 2.0
Humans are testing the limits of most species’ survival, with their planet-wide changes. As urbanisation, deforestation, loss of wildlife, and human-wildlife conflicts continue to spiral up, there is a need to use every available tool available, to help protect what is left of the natural world. Molecular ecology is one such tool for conservation and can help in wildlife disease management and forensics in illegal trade.
What is molecular ecology?
Molecular ecology is a hybrid field that combines molecular biology techniques with ecological data to make sense of natural processes such as the growth or decline of populations, formation of new species, extinctions and invasiveness.
In modern molecular ecology, genetic data is analysed in the context of field and observational studies to address ecological problems.
Molecular ecology is used to estimate population genetic diversities to aid wildlife breeding and conservation efforts, define species for conservation policy, track diseases and combat poaching.
What are genetic data and population genetic diversity?
Genetic data from organisms is collected in the form of ‘molecular markers,’ which are biological molecules that may be used to distinguish between species, populations, or individuals.
When molecular biologists first began identifying genetic differences between individuals, they extracted proteins from animal or plant tissues, and used them as molecular markers. However, DNA-based markers soon became more popular than protein markers as they could be obtained from very small samples of tissue. They were also easier to handle and showed more variations than protein-based markers. Molecular ecology now relies on extracting DNA from animals using tissue samples (typically hair, scales, skin, bones, horns, or blood) or even fecal matter.
Different individuals within a species can have different forms or variants of a particular gene or molecular marker. A familiar example of this is blood type – one of the genes that determine blood type in humans comes in three different forms/variants known as A, B and O. Such genes are known as polymorphic (‘poly’ = many, ‘morphic’ = form) genes. Genes that are the same in all individuals of a population are called monomorphic (‘mono’ = one, ‘morphic’ = form).
By studying and documenting the variations in the genes and molecular markers, one can measure the genetic diversity of a population of animals with the help of statistics.
Why is genetic variation important for wildlife breeding and conservation efforts?
Genetic diversity is the fuel for natural selection. It is a source of inheritable variations in characteristics that can allow populations to survive changing environments. Higher the genetic diversity of a population, higher the chance that some individuals in that population can adapt to new environmental conditions. Thus, the population will not go extinct due to any changes.
Large populations typically have high genetic diversities, whereas small populations have low genetic diversities. If the population size of a species drops sharply due to natural disasters or human negligence and anthropogenic activities, its genetic diversity is reduced, creating a genetic bottleneck. When this happens, not only is the population robbed of its potential to survive, it also becomes vulnerable to inbreeding. Inbreeding occurs in small populations, where genetically related individuals are more likely to mate with each other.
Over time, such populations suffer from ‘inbreeding depression’, a condition where genetic variants with harmful mutations begin to accumulate.
Cheetahs are a classic example of how inbreeding depression can bring a species to the brink of extinction, despite extensive efforts at conservation through captive breeding programmes. To understand why captive breeding efforts in cheetahs were failing, a series of genetic analyses were conducted. These analyses showed that due to the combined effects of the past natural disasters and indiscriminate human hunting, cheetahs were highly inbred.
The inbreeding not only caused reproductive issues with low fertility and high infant death rates, but also left cheetahs vulnerable to diseases. The cheetah’s genetic diversity was so severely decimated, that a crucial immune-related gene complex, which is usually very polymorphic in most species, was monomorphic (had no genetic variation) in cheetahs. This caused feline infectious peritonitis – a common viral disease that kills fewer than 1% of domestic cats – to wipe out nearly 80% of a captive breeding population of cheetahs in the US.
To offset inbreeding in captive and protected populations of other endangered species (Mexican red wolves, Puerto Rican crested toads and African lions, to name a few), conservationists have attempted ‘genetic rescues’. Genetic rescues are carried out by introducing new individuals (which can add more genetic variation) into inbred populations to increase genetic diversity.
However, such measures can backfire in some species like the Ibex and the Arabian oryx, which ironically, suffer from ‘outbreeding depression’. Gene flow between populations in such species is usually low, as their populations are insular with very limited immigration and emigration; therefore, each population seems genetically inbred. This, however, is advantageous for the population as it has developed ‘local adaptation’ and maintains a specific combination of gene variants that allow for better survival in local conditions.
In misplaced attempts at genetic rescue by reversing this local inbreeding to ‘recover’ genetic diversity in such systems, breeding programmes mate individuals from different populations. The outcomes of these efforts are usually poor. The offspring of such pairings often end up with genetic combinations that leave them unable to survive in either of the two local conditions. For example, in an attempt to genetically rescue the Alpine ibex, Nubian ibex were introduced into the Tatra mountains. Unfortunately, the introduced ibex which were adapted to warmer climates, rutted in autumn and birthed hybrid young in February, the coldest time of the year. Obviously, these offspring did not survive, and the rescue attempt failed.
Based on the lessons learned from both inbreeding and outbreeding depression, it is clear that molecular ecology is essential for successful wildlife conservation.
In India, molecular ecology studies on the critically endangered gharial and blackbuck reveal that the genetic diversities in managed populations of these animals are not high, painting a grim picture for their chances of survival.
Recent work using genome-wide data on tigers suggests that compared to the tigers from Amur, Sumatran, and Malayan populations, Indian tigers have very high genetic diversity. However, this data also indicates that certain tiger populations in India are so isolated and small, that local inbreeding is occurring.
“Although we have many tigers in India – roughly two-thirds of all the world’s tigers – their populations in some parts of India are fragmented, which has caused local inbreeding. The Amur tigers, on the other hand, are much fewer in numbers, but they are not inbred because they are not isolated from each other,” says Uma Ramakrishnan, a molecular ecologist from the National Centre for Biological Sciences, Bengaluru.
Ramakrishnan and her team have worked on tigers for over 15 years, and their molecular data is now being used to formulate plans for genetically rescuing some of India’s inbred tiger populations. “Our work can help collecting data regarding which tigers are least inbred and which ones can be moved between populations,” she adds.
How can molecular ecology-based species definitions help in conservation policy?
Defining a species seems more like an esoteric academic undertaking rather than a serious and practical conservation issue. However, the conservation status of a species and the legal protection it is accorded is based on its taxonomic classification. Therefore, any ambiguity in how or what constitutes a particular species can have a major impact on that organism’s survival.
Traditional methods of defining a species based on physical characteristics and behavioral observations are no longer considered reliable. Molecular taxonomy, which depends on genetic information, is now being increasingly used to resolve taxonomic disagreements and correct misclassifications.
Errors in taxonomy have resulted in the mismanagement of conservation efforts of many species. Two examples that stand out, are the cases of the colonial pocket gophers and the dusky seaside sparrow.
A single population of pocket gophers (<100 in number) within a tiny range in the State of Georgia, USA, was managed as an ‘endangered species’ for more than 10 years as it was described as a ‘distinct species’ (Geomys colonus) based on physical characteristics. Molecular ecology later proved that this population was genetically no different from Geomys pinetus, a pocket gopher species that is common in southeastern USA.
Similarly, when a darker form of the seaside sparrow (Ammodramus maritimus) was discovered in Florida, it was identified as a separate species (A. nigrensis) and listed as endangered due to its low numbers and restricted range. After a seven-year long unsuccessful captive breeding program, the last dusky sparrow died in captivity. Two years later, however, molecular data revealed that this ‘species’ had been genetically indistinct from the seaside sparrow.
In both these cases, conservation efforts were wasted on populations that had been misclassified as distinct species.
Another area in which molecular taxonomy is becoming important is in identifying areas rich in endemic species.
“India has a huge amount of biodiversity, but many of its landscapes, like savannahs, and organisms, like arthropods, have hardly been studied. Now, with more field expeditions across these landscapes, and better taxonomic tools based on DNA that complement traditional morphology-based classification, we are making some surprising discoveries in the field of systematics,” says Jahnavi Joshi, a molecular ecologist and taxonomist from the Centre for Cellular and Molecular Biology, Hyderabad.
Recent studies on the molecular taxonomies of geckos and centipedes have shown that previously ignored regions like peninsular India, the Eastern Ghats, and the drier northern parts of the Western Ghats are unexpectedly rich in endemic species. Such areas need to be protected to conserve the range-restricted flora and fauna that are exclusively found there.
How is molecular ecology useful in detecting and managing diseases in wild animals?
Molecular ecology has now become an important part of wildlife disease management. Rapid detection of even low intensities of viral, bacterial, and parasitic infections is now possible using tests based on PCR (polymerase chain reaction – a technique that ‘amplifies’, or makes more copies of, specific DNA regions). Currently, PCR-based diagnostic tests allow for the swift detection of a number of diseases in wildlife such as the Kyasanur forest disease (a tick-borne viral disease in South India), Ebola, Nipah, tuberculosis, rabies and malaria, all of which are directly responsible for endangering wildlife and spilling over into domestic livestock and human populations.
By studying molecular interactions between pathogens and their vectors (insects like ticks and mosquitoes, or wildlife like raccoons), scientists can even track routes of transmission and reservoir hosts for diseases such as monkey fever, avian malaria and rabies. In addition, molecular ecology studies on host-pathogen interactions can help conservationists understand how some species or individuals are more tolerant, resistant or susceptible to certain diseases.
For example, molecular genetics work on frogs is showing that individuals with stronger immune systems are actually more likely to die of chytridomycosis, a fungal skin infection that has caused mass die-offs and extinctions in amphibians globally.
How do genetic trails aid in anti-poaching efforts?
When law enforcement authorities seize illegal wildlife products, the first problem they encounter is identification – what animal does a pelt, skin, hair, horn, flesh or bone belong to?
Molecular forensics using DNA barcoding has been used to identify species even from processed samples such as dried meat and powdered bones or horns. Similar to how supermarket scanners can identify products from a series of black and white stripes using the universal product code, DNA barcoding matches short sequences from samples with those in a reference database to identify which species the sample belongs to. For animals, sequences from the mitochondrial gene COX1 or CO1 (cytochrome oxidase 1) are usually used. Currently, reference databases such as the Barcode of Life Data System and the International Barcode of Life contain nearly 9.5 million DNA barcodes for thousands of species of animals, plants, and other organisms.
The usefulness of molecular tools does not end there. Other molecular markers such as microsatellites, minisatellites and single nucleotide polymorphisms, as well as techniques such as DNA profiling/fingerprinting (which has been used in criminal investigations), can be applied to identify which country or population the poached animal came from. Researchers have used microsatellite data to identify the species, sex and even geographic origins of seized tiger parts, elephant tusks and a variety of other animal parts.
This article was originally published by Mongabay-India and has been republished here under a Creative Commons license.