Is genetic diversity worthy of conservation?

There is a debate on (1) whether genetic diversity is related to population fitness, (2) how to predict fitness using genetic measures and (3) whether population size is important to fitness. In 2003, in an attempt bring clarity to this debate, David Reed and Richard Frankham (Macquarie University, in Sydney) published an article in Conservation Biology. They carried out a meta-analysis of all studies that measured some form of fitness related to molecular data, quantitative genetic data and population size. Although the number of studies that were available for analyses were insufficient to give robust conclusions, they believe there to be enough evidence to support their conclusions; heterozygosity, quantitative genetic variation and population size were significantly correlated with population fitness.

Not only does this article clearly explain the issues surrounding the reasons why genetic diversity is integral in species conservation, Reed and Frankham justify their conclusions with empirical evidence. I recommend that this article should be read by all those interested in conservation biology, especially those that are not directly concerned with biodiversity genetics.

The World Conservation Union (IUCN) recommends that as part of conserving biodiversity, genetic diversity must also be conserved. The IUCN justifies this with the following two reasons: (1) genetic diversity is required for populations to evolve in response to environmental changes and (2) heterozygosity levels are linked directly to reduced population fitness via inbreeding depression. -- A heterozygous population is one with a maximum level of allelic variation at a given locus and inbreeding depression is caused by the breeding of closely related individuals, and leads to increased homozygosity (or reduced heterozygosity).

Thus, if genetic diversity is not managed, or maintained in small or declining populations, (1) the population may not respond to particular environmental changes and (2) increased inbreeding might send the population to extinction, as in Graeme Caughley’s extinction vortex theory.

In their argument, Reed and Frankham explain that although heterozygosity and fitness might not be related --(because (1) molecular markers used to estimate heterozygosity may not affect fitness, (2) of non-additive genetic variation (where phenotypic variation is caused by the interaction of genes at several loci), and (3) increased selection against homozygotes may purge deleterious alleles), they found that heterozygosity, population size, and quantitative genetic variation were positively and significantly correlated with population fitness.

So, how can this theory be applied to conservation management practice? Firstly, methods for simple, non-invasive collection of genetic material from endangered species must be optimised. The following DNA extraction and analysis must also be quick and inexpensive, so that multiple analyses can be carried out. Often, it is difficult to keep pedigrees for wild species, so efficient methods that prove relatedness and define within-generation variation could help conservation managers maximise genetic variation within populations and between generations. Furthermore, it is expected that in the near-term, genome sequencing will become relatively straightforward and cost-effective. This will allow the definitive calculation of genetic variation between individuals and for populations. Unfortunately, it will not be as easy locating specific genes that directly affect fitness. 

Reed and Frankham suggest that the migration of individuals to a population greatly increases heterozygosity. This could be managed in captive and wild populations; furthermore, if conservation managers know which genes are fixed in the population, individuals that are known to have a heterozygous copy of that gene could be introduced to that population. However, the take-home message from this article is that population size must be maximised for species to evolve in response to environmental changes and to reduce the negative effects of inbreeding depression.

Photo: The takahe is one such species whos genetic diversity is thought to have been reduced by inbreeding depression.   

Red spot on the Retina?? Could be fatal TSD!!

Tay-Sachs disease (TSD), a rare genetic disorder is also called as Hexosaminidase A deficiency and is innate in an autosomal recessive pattern (where both copies of the gene in each one cell have mutations). The disease is named after an ophthalmologist ‘Warren Tay’ (British by origin) that firstly described and identified the red coloured spot on the retina of the eye in year 1881 and there after an American neurologist B. Sachs primarily explained the cellular changes involved in TSD. This disease is caused when unfavourable quantities of ganglioside, a fatty acid derivative mount up in the nerve cells of our brain. Further researches in late 20th and early 21st centuries verified that TSD is caused due to the mutations on the HEXA gene on chromosome number 15. This HEXA gene supply instructions for the formation of a part of beta-hexosaminidase A enzyme, located in lysosomes and have a crucial role in the spinal cord and brain. A large number of HEXA mutations have been discovered and advanced researches are still going on and a fact which came into light is that most of the HEXA mutations are extremely rare and do not occur in genetically isolated populations. Most of the cases are found in people of central and eastern European countries especially in Cajun and Amish community in Louisiana and Pennsylvania.
TSD can occur at any age and stage but the most common one is in infancy. Both the parents carry one copy of mutated gene each, but may or may not show symptoms of this condition. These mutations in the HEXA gene upset the functioning of beta- hexosaminidase A, which avert this enzyme from breaking down GM2 ganglioside resulting into its accumulation up to a toxic level in brain and further causing problems.
Broadly TSD can be divided into three levels depending upon the age at which it occurs:

Infantile TSD
Disease becomes noticeable after first six months of life resulting into muscle atrophy and paralysis. Death occurs before the age of 4-5 years

Juvenile TSD
Very rare case when disease appears in the age group of 2-10 years followed by speech, motor and swelling difficulties. Death occurs between 5-15 years of age.

Adult TSD
Rare form of TSD occurs in the age group of 20- 30’s followed by neurological weakening, unsteadiness of gait, psychiatric illness like schizophrenia resulting into restricted movements and physical complications.

A child can have Tay-Sachs disease only & only if both the parents are carrier of the genes. When two carriers have a child together i.e (MCarrier x FCarrier)
50% possibility that their infant will be a carrier(ICarrier), but not have the disease
25% possibility that their infant (IDisease ) will have the disease
25% possibility that their infant (I Healthy ) will not be a carrier and not have the disease too.

Location of HEXA gene: positioned on the long (q) arm of chromosome 15 between 23 & 24 positions.

U.S. National Library of Medicine®

There is at present no cure for TSD. After an extensive medical care too, children with infantile TSD suffers and die by the time they reach the age of 5 or 6 and the sufferings in Adult TSD can only be slowed down with the help of drugs and treatments. Various methods of treatment like Substrate reduction therapy, Gene therapy, Enzyme replacement therapy (Gregory M. Pastores, 2006) is still under experimental stages. Anticonvulsant medicine might primarily manage seizures. Other compassionate cure includes apposite nutrition and hydration and techniques to carry on the airway open. Children may ultimately need a feeding hose or pipe.



Click here for more details and for comprehensive reading about the Tay-Sachs disease

THE COMMON NEW ZEALAND DOLPHIN

The knowledge of the common dolphin in New Zealand is very less, and very little authentic information is available for the species which occur in Hauraki Gulf. Delphinus sp.,the common dolphin species, native to New Zealand, have been misunderstood in terms of habitat use and demographics which has led to inadequate recognition and management of New Zealand Delphinus. These dolphins are the most abundant cetacean species in the Hauraki Gulf and this study was undertaken by Karen A Stockin and associates understand the effects of diel, season, depth, sea surface temperature, group size, and composition and dolphin behaviour. The activity budget of the dolphins was studied with respect to their activity stages- forage, mill, rest, social and travel and the compared with the earlier studies done by Dirk R. Neumann in 2001.

A semi-enclosed body of temperate water, of 60m maximum depth, was chosen as the study area, which is on the east coast of North Island (Hauraki Gulf, NZ). Due to the subtropical East Auckland Current, it as believed to be highly productive area with high levels of nutrients and large diversity of biological fauna. The studies were done on 92 samples analysed for 577 base pairs of the mtDNA control region. The samples from New Zealand were then compared with the published results from eight other populations around the world. Data was collected from Feb 2002 to Jan 2005.

The data was collected in relation to seasonal patterns in the activity budget and environmental variables were taken into account. Water depth and temperature was analysed in raw data. Behaviour studies were recorded by taking the initial and the lagged behaviours of the dolphins were taken into account (Lagged- after 30 minutes of viewing the dolphin).

The results showed that behavioural data was collected for 686 groups out of total of 719 dolphin encounters. The activity budget for forage and travel were the most recorded states and social and rest were the least recorded behavioural states. Foraging was most recorded in winter and spring whereas resting was recorded in winter and autumn. Behaviour varied with the depth, foraging groups were observed in deepest, resting groups in shallowest, and travel and socialising groups were observed in median water depths. It was observed that the temperature also played a role in their behaviour. The foraging groups were observed in coolest (17.9°C), resting groups in warmest (20.3°C) and travelling, socializing and milling groups were observed in median temperature of 19.3°C.

Common dolphins observed in the Hauraki Gulf, New Zealand during assumed copulation. Photograph by Karen Stockin.

The results concluded that the behaviour of the common dolphins were most influenced by water depth and food availability (46.8%) and determines their activity budget.

This paper presents the evidence that common dolphins occur in Hauraki Gulf due to availability of food and dolphins inhabit this area for other biological processes. This study shows that it is an important area for the Zealand Delphinus as it allows them to spend little time travelling and getting food and get more time in foraging, resting, breeding and tending calves. More deepening ecological studies will provide a platform to develop more action oriented strategies to wise management of the marine resource which is under stress from the local urban density and its use for recreation.

For more information: Marine Mammal Science, Volume 25 (2), April 2009

What's in your dinner?

Insectivorous bats use echolocation to move around their surroundings and to locate prey. In response, some insects use hearing-based defences to detect and evade echolocating bats. Furthermore, some arctiid moths produce ultrasonic clicks in response to bat echolocation calls and thus deter bat attacks or advertise their unpalatability. Therefore, there is always a constant evolutionary arms race going on between predator and prey.

To infer predator-prey relationship is not easy, especially when predation is hard to document or observed directly. Traditionally, identification of digested prey remains is by using visual morphological analysis. This can be of a problem, because insectivores chew up their prey rapidly and thoroughly, and of course when the prey goes through the digestive system, nothing much remain except for exoskeletal parts. Therefore, in the past, morphological identification rarely went lower than orders. Thus, molecular techniques can come in quite handy when morphological identification fails.

With the improvement in technology, molecular approaches have provided new opportunities to characterise predator-prey relationship in complex food webs. The techniques have assisted in prey identification, often very accurately to species level. Furthermore, this is considered a non-invasive sampling method, as it is only a small part of the study subject that is taken, and in this case, bat guano.

Eastern red bats (Lasiurus borealis) range across most of eastern North America. They frequently forage around streetlights where there is a large concentration of insects. These bats have extremely robust jaws, similar to other bats species that specialise in Coleoptera (beetles) prey, which have a hard case to protect against predators. Furthermore, the bats also emit echolocation calls between 30-65 kHz, making them audible to tympanate insects.

Clare et al (2009) employed molecular techniques to describe the diet of the eastern red bat, Lasiurus borealis, and test several existing hypothesis about the prey of these bats. This is the first time Polymerase Chain Reaction (PCR) and sequence-based approaches for dietary analyses have been done on bats. The results were compared with the North American arthropod database present in the Barcode of Life Data System.

What they found from the study was, despite having an extremely robust jaw, L. borealis’s diet consists of a wide range of insects, but mainly of soft-bodied Lepidoptera species (butterfly and moths). They also identified insects from other orders that were not detected from previous studies using just morphological identification. More surprisingly was that most of the Lepidopterans that were preyed on were tympanate species, which means they had “ears” they use to detect echolocation used by hunting bats. It would seem like the bats are winning the arms’ race!!

This goes to show that by looking at the morphology or behaviour of predator species alone is not enough to infer the range of prey that they take. The authors also reported that several economically important pest species were found in the bat’s diet. This might be an important implication for pest management as it would be interesting to see how much of the pest species constitute the bat’s diet. Also, this type of study could also be used to infer relative abundance of pests.

Molecular technology breakthrough can provide a whole new level of understanding of the evolutionary and ecological principles underlying food web relationships.

Click here for more details and in-depth reading about the Eastern Red Bats and their diet

Vicariance versus Dispersal: Chatham Islands

The flora and fauna composition of the Chatham Islands is distinctive from the New Zealand mainland and includes many endemic species. The uniqueness of these endemic species has arisen due to the 800 kilometres of open ocean separating the Islands from the mainland. There are multiple theories regarding the origin of the ancestors of Chatham Islands biota. The vicariance theory explains the cause of speciation as the separation since the areas were geographically connected in the past (now separated by plate tectonics). The dispersal theory states that founding taxa historically crossed a significant barrier by dispersal and the difference has arisen due to the subsequent separation. In the past, testing of these theories has been based on morphological differences. With the combination of the relatively new techniques of DNA sequencing and molecular clocks, the time period when species divergence occurred can be estimated, allowing better testing of these theories.

A study by Steven Trewick in the paper ‘Molecular evidence for dispersal rather than vicariance as the origin of flightless insect species on the Chatham Islands, New Zealand’ investigated the origin of Chatham Island biota using mitochondrial gene sequences to test the vicariance versus dispersal argument. The study had three main hypotheses for the origin of Chatham biota; Gondwanan vicariance, vicariance created by the loss of a land bridge, and recent oversea dispersal.

There are multiple theories regarding the most recent connection to the mainland. The Chathams may have adjoined the mainland in Gondwanan times over 70 million years ago. For the current fauna to have Gondwanan origins, the theory has to assume that the Chathams area did not submerge since disconnection. A more likely theory is that a post-Gondwanan land bridge may have existed linking the Chathams and southern New Zealand, that has since submerged. This theory is supported by the fact that high endemicity is primarily at the species level, implying relatively recent biological isolation of the Chathams.

For the study, genera found both on the Chathams and the mainland that contain large flightless species were selected . Taxa with these characteristics are expected to have a low dispersal ability over sea, making them susceptible to vicariance. Therefore, this was expected to exclude dispersal as a cause of origin, better testing the vicariance hypotheses. Two beetle genera (Mecodema and Geodorcus), a cave weta genus (Talitropsis) and one cockroach genus (Celatoblatta) were selected for the study. Within the selected genera, samples of all available species from the Chathams and species present at sampling locations on the mainland were collected for analysis. The mitochondrial gene, cytochrome oxidase 1 (CO1) was used as the source of the DNA sequences for the comparison.



Geodorcus spp. stag beetle exemplifying the large size and flightlessness of this genus. (Photo: Ian Phillipps)


It was found that the Chatham Islands taxa are closely related to New Zealand taxa and in the case of Mecodema, are not genetically separable as distinct species. Chatham diversity appears to be a subset of New Zealand diversity with all genera colonising the Islands over one time period. This episode of colonisation was estimated using the observed divergence within the genera and the standard molecular clock calibrations of 2–2.3% sequence divergence per million years. It seems that the colonization occurred within the Pliocene period from 2-6 million years ago, discounting the Gondwanan vicariance hypothesis.

With the important addition of a colonisation time frame, the land bridging hypothesis can also be discounted, as geology has so far failed to reveal evidence of any such structure during the Pliocene. Therefore, the ancestors of current taxa seem to have arrived by oversea dispersal. The study targeted taxa with little potential for active migration over water. However, it may be that the genera have a susceptibility to passive dispersal. Mecodema and Geodorcus beetles have their larval stage within decaying logs, and Talitropsis and Celatoblatta often have their daytime roosts in logs. Therefore, it is possible that these insects travelled to the Chathams in floating logs.

The lack of deeply diverging lineages among the studied genera may be caused by pre-Pliocene submergence of the island group. This could have removed the species that occupied the Chatham Islands before the current biota colonised. Therefore, despite the new revelations allowed by molecular techniques, it can only be concluded that the current observed biota of the Chathams arrived by dispersal. The origin of biota that possibly preceded the suggested submergence event still remains unsolved.

The full article for the study can be found in the Journal of Biogeography, volume 27, issue 5, pages 1189-1200. A link to the article can be found here.

Assessment of maternal migration for hector's and maui dolphins

There are two sub-species of hector's dolphin, Cephalorhynchus hectori (South Island hector's dolphin) and C. hectori maui (maui dolphin). These dolphins are endemic to the relatively shallow waters of New Zealand (within four nautical miles of land). They can be commonly recognised by their small size, black rounded dorsal fin and grey bodies with black and white markings around the snout. Various populations of the South Island hectors dolphin exist scattered around the east, west and southern coast of the South Island, while the only population of maui dolphins can be found on the west coast of the North Island.

South Island hector's dolphin. Photo by Tewhaipounamu, flickr.

The South Island hectors dolphin is considered to be endangered with an estimated population size of 7270 individuals. The maui dolphin is thought to be critically endangered with an estimated population size of 111 individuals. Both sub-species populations are in decline, mainly due to the effect of entanglement in gill nets.

It was generally thought that there was minimal migration between various South Island hector's dolphin and maui dolphin populations; however it was important to assess whether these populations were genetically isolated. The study "Geographic isolation of hector's dolphin popilations, described by mitochondrial DNA sequences" carried out by F B Pichler, S M Dawson, E Slooten and C S Baker, had the aim of using this information to identify the appropriate population units for management.

Samples were taken from a total of 34 individuals which had been found beachcast or accidentally caught in gillnets. Of the 34 individuals, 20 were from the east coast of the South Island, 12 from the west coast of South Island, and 2 from the North Island (at the time maui dolphin had not yet been recognised as a separate sub-species). A section of mitochondrial DNA (mtDNA) known as the control region was isolated and sequenced. The control region was used because it is known to be highly variable in other Cetacean species, and is therefore a good measure of the isolation of populations.

The mtDNA sequencing showed 13 polymorphic sites, with 11 distinct mtDNA haplotypes in the control region. This mtDNA control region showed a 0.28%-1.67% variation between different populations of South Island hector's and maui dolphins. Finally there was a 0.659-0.929% variation within local populations of South Island hector's and maui dolphins. The results also identified three distinct clades, one on the east coast of the South Island, one from the west coast of the South Island, and a third clade found in the maui population from the North Island.

From these results a number of conclusions can be drawn. The different haplotypes found in each population, distinct clades and higher variation between populations than within populations all indicate a lack of maternal migration between populations. As there is no known geographical barrier to inhibit migration, it is thought that this is due to ecological preferences and a strong sense of philopatry (when an individual returns to its birth place to breed). This level of isolation between populations is unusual for Cetacean species. However, this method only gives an indication of maternal migration, as mtDNA is only passed down maternal lineages. To get an idea of the true level of isolation further investigations should be conducted into nucleic DNA and male movement patterns; however it is thought that male migration between populations is also minimal.

There are a number of implications that come from these conclusions. If this genetic isolation continues, individual populations will continue to become genetically dissimilar from one another. Another implication is due to the small size of isolated populations and lack of gene flow, it is likely that the each population's gene pool will decrease and genetic variation will get lower and lower. This could potentially create an inbreeding depression and effect their survival. This isolation also means that if a local extinction occurs, populations will be very slow to recover as recruitment from outside females is low.

These results also quantified these populations as independent stock, defined by demographic criteria (migration between populations is less than reproduction or natural mortality within a population). The significant divergence between allele frequencies of mtDNA also qualified the sub-species to be considered independent genetic management units. From this, the recommendation was made for separate conservation plans for east and west coast South Island populations. They then went on to recommend maui dolphin be considered a separate management unit and since the study, maui dolphin have been recognised as a separate subspecies.

Two or three freshwater crayfish species?

The freshwater crayfish, or koura (Maori name), is a crustacean from the genus Paranephrops which is endemic to New Zealand. Koura are very important to the functioning of freshwater ecosystems as they recycle leftover materials through their scavenging, help filter fine sediments from the water and also act as an indicator species, signalling to scientists when
conditions in a stream or pond are unfavourable.

Koura are currently officially recognised as two distinct species, the northern koura Paranephrops planifrons and the southern koura Paranephrops zealandicus. However, recent work in the field of molecular genetics has resulted in some illuminating insights into whether there is just two species, or maybe more!

Smita Apte and Graham Wallis from Otago University and Joshua Smith from NIWA collected mitochondrial DNA samples from 76 sites and 182 koura throughout New Zealand with the aim of investigating whether the Southern Alps and Cook Straight have any effect on the shaping of genetic structure within Paranephrops.

The mitochondrial DNA marker cytochrome oxidase subunit I was the marker used in the analysis. Sequencing and subsequent analysis actually showed three distinct koura lineages as opposed to the two species which are currently described. The southern koura was shown as being just one species while the northern koura was split into two distinct groups; koura in the North Island and Nelson and Marlborough region and koura on the southern West Coast and rest of the South Island. So, the Southern West Coast portion of the species believed to be P. planifrons is actually more closely related to P. zealandicus than the species it is currently classified as being a part of.

These results indicated that the the mountain building of the Southern Alps provided an important geographic barrier between the West Coast haplotypes and the Eastern South Island haplotypes so that speciation could occur. However, this is not over the whole of the Southern Alps range because koura on the outhern West Coast were found to be more genetically similar to the northern koura than the other West Coast haplotypes. This results in a threefold genetic structure, with a seperation essentially into northern, central and southern koura lineages.

This has some broad implications for the future conservation of the treasured koura in New Zealand. Koura are currently listed as threatened species and their populations are in gradual decline due to habitat destruction, predation by introduced species and over-harvesting by humans. With this genetic work uncovering three distinct genetic species, the classification of koura needs to be reconsidered to include these three species. Furthermore, conservation initiatives now need to consider three species instead of just two.

The original paper, which was published in Molecular Ecology, volume 16, pages 1897-1908, can be found here.