Monthly Archives: Nov 2014

Comparative population genomics in animals uncovers the determinants of genetic diversity

Countless research has provided evidence of genetic diversity being a central component to many conservation challenges. Being able to predict species diversity is therefore a very beneficial strategy which is what this paper aims to investigate. So far the main focus of conservation has been directed on large sized vertebrates. However these popular animals have been shown to represent a very small subset. This study aims to investigate nucleotide diversity of a larger representation of all species which includes the invertebrates. From this we can uncover whether we can predict genetic diversity of a species.

The gap for molecular data across invertebrates still needs to be filled and the first distribution of genome wide polymorphism levels across metazoan trees of life have been presented, 31 Families of animals spread across 8 animal phyla. For 10 individuals in each family high coverage transcriptomic data was produced and a very weak relationship between nucleotide diversity and any of the geographic variables studied were found. Conversely the body size of the stage that an offspring leaves its parents is by far the most predictive variables. Overall the analysis of the paper indicates that species diversity can be predicted by the number of offspring and longevity of a species. The paper also shows that long lived species with a high brooding ability were shown to be less genetically diverse than short lived species.

The study acknowledges the central population genetic theory that a higher effective population size gives rise to higher genetic diversity and shows how empirical evidence gathered from RNA seq data does not support this. A weakness of the study is that it does not mention the impact of crowdedness of ecological niche on reproduction strategy.

Often organisms do not fall neatly into the strict categories of either producing few offspring and being short lived or producing more offspring and being shorter lived, we feel that ecological life histories could be viewed more as falling along a spectrum.

Species that produce small numbers of offspring and have high longevity have lower genetic diversity which could put them at risk. However the strategy of having many offspring has more risks associated with it, as their “quality” is not equal to the offspring of the lower fecundity strategists. The low fecundity strategists have the advantage of being well selected for their environment and thought to be more resistant to changes within it.

Presently, species conservation often prioritises the rare species ,whether endangered or endemic, and focuses on areas deemed as having a high level of biodiversity (large numbers of different species per unit area). This study encourages us to look beyond the species that are already defined as being endangered and to ones that could become wiped out very quickly due to lack of genetic diversity within the species population. Genetic diversity provides populations with resistance to changing environments and  diseases. The ecological strategy of a species could now become a factor in prioritising species for conservation, where DNA data is not available.

The study used extensive evidence and used a variety of  non-model organisms. In future studies more organisms could be included. From having a clear pre-understanding of the future diversification of species, extinction can possibly be avoided.

References:

Romiguier, J, Gayral, P, Ballenghein, M, Bernard, A, Cahais, V, Chenuil, A, Chiari, A, Dernat, R, Duret, L, Faivre, N, Loire, E, Lourencho, J.M, Nabholz, B, Roux C, Tsagokogeorga, G, Weber, A.A-T, Weinert, L.A, Belkhir, K, Bierne, N, Gelemin, and Galtier, N 2014 ‘Comparative population genomics in animals uncovers the determinants of genetic diversity’ Nature doi:10.1038/nature13685

Genome chronicles – The Giant Panda’s (hi)story

by Luca Dellisanti & Megan Saul

The Giant Panda, native to China and its surrounding South-Eastern countries, is at great risk of going extinct. An interesting study led by S. Zhao from the Chinese Academy of Science in Bejing has given a deep insight on the evolution of the species from 8 million years ago to the present day. The first of its kind, this study looks at the genetic makeup of 2% of the total world population of living wild Giant Pandas, a much larger study than any previously attempted. The size of this study has made it possible to identify three distinct populations for the first time.  It highlights something quite remarkable. This study helps us understand how the populations were formed through a variety of bottlenecks, expansions and divergences as a consequence of climate change and human activity. In the last 3000 years humans might have had more of a detrimental impact than 8 million years of climate change.

The fossil record of China and its surroundings provides evidence for three ancestral species of panda living in the area in the past. Their struggle for survival has been great and the species evolved a bigger body size, better suited to cold climates. They also switched their dietary preferences. Previously carnivores, pandas became more reliant on bamboo as a staple. Whole-genome sequencing has been used to look at the past history of the species and revealed two major events of dangerous population decline. Very interestingly, the timings of the two declines, respectively 200 and 20 thousand years ago have been found to correspond to periods of cold and dry climate, poor conditions for bamboo (see Fig. 1).

Fig 1. Demographic history from the panda's origin to 10,000 years ago, showing two expansions followed by two bottlenecks (blue and red lines). Change in climatic conditions is shown with the thin borwn line. High values represent cold and dry conditions, low values indicate warm and wet conditions. The approximate chronological ranges of three fossil panda species or subspecies (primal, pygmy and baconi panda) are shaded in pink, orange and blue, respectively.
Fig 1. Demographic history from the panda’s origin to 10,000 years ago, showing two expansions followed by two bottlenecks (blue and red lines). Change in climatic conditions is shown with the thin brown line. High values represent cold and dry conditions, low values indicate warm and wet conditions. The approximate chronological ranges of three fossil panda species or subspecies (primal, pygmy and baconi panda) are shaded in pink, orange and blue, respectively.

A variety of techniques and programmes were used to infer past information about the panda genome. After the initial whole genome sequencing of several living individuals the patterns of occurrence of SNPs (point substitutions of nucleotides in the DNA) from each individual were compared and genetic relationships highlighted. This along with further analysis helped separate out 3 populations: Qinling (QIN), Minshan (MIN) and Qionglai-Daxiangling-Xiaoxiangling-Liangshan (QXL).

Positive selection was found to have acted on functional genes related to bitter taste in the QIN population. These pandas eat more bamboo leaves, known to be bitter. Many olfactory receptor genes are also shown to be under balancing and directional selection. This is particularly relevant as pandas use these senses to locate others in the forest so is important for panda reproduction and survival. MIN and QXL compared to QIN and non-QIN populations were found to have less variation.

The study has helped us gain a better understanding of the living panda population which could be crucial in conservation efforts. The writers suggested re-introducing captive pandas into the wild to boost population numbers but they may struggle to survive in the wild and constant monitoring would be necessary. We are now aware of strong impact humans have had in the recent years on population decline and of the role we have played in dividing current populations into smaller, more at risk groups. We can no longer solely blame climate change for the decline in populations. If we are to make a marked attempt to conserve the giant panda more needs to be done to study the populations at a local level and people living in these areas need to be aware of the effect they are having on the giant pandas.

Figure and content from Zhao et al, Nature 2013