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.   

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.