Category Archives: Conservation genomics

Genome-wide signatures of convergent evolution in Echo locating mammals

by Daniel Considine

 

Most people understand that evolution, for the most part, works in a divergent way. This concept is fairly easy to grasp. When some form of reproductive barrier is introduced to a population, drift and many other factors will take over. When given enough time this will result in the two separated populations diverging to the point where they are now two completely different species, this is the fundamental process of divergence. What is not so intuitive is when two completely distinct species both independently evolve similar features. This is referred to as convergent evolution, and there are some notable examples. The most commonly cited example is how birds and bats both evolved the ability of flight. This is known as an analogous trait, where in two unrelated species face similar environmental challenges and both arrive at the same solution. Analysis of the anatomy of these species makes it clear that their wings are related in no way besides function.

Until recently, researchers were unsure of how convergent evolution worked, if at all, at the molecular level. One major breakthrough was in the analysis of amino acid substitutions at the active site of protease enzymes of different species. A recent paper in Nature (Parker et al, 2013) demonstrated how the nucleic sequence of completely unrelated species show convergent evolution at the site of functionally similar genes. Evidence suggests that echolocation has arisen at three independent times; once in whales and twice in bats. What is truly remarkable about these findings is that in all three instances, there are far more convergent amino acid substitutions to genes involved in hearing than would be expected by chance.

Researchers took 4 distinct bat species, consisting of both echo locating and non-echo locating species, and sequenced their genomes. To align these sequences, they took a further 18 mammal genomes from databases, one of which was the echo locating bottlenose dolphin, to make comparisons. Analysis of this data showed that genes involved with hearing, and in particular those which are important for echolocation, showed similarities with a very high likelihood of convergent evolution. To compound this finding, analysis was also carried out on the genes involved in vision, as bats and dolphins have both undergone adaptation for low-light environments. Again researchers found that the amount of similarities across these sequences strongly supported the hypothesis that convergent evolution was taking place. Finally, analysis of the nature of nucleic sequence substitutions was carried out. This analysis showed that these loci were under strong selection, which adds to the evidence of a convergent theory. One criticism of this methodology however, is their lack of comparison to a non-echolocating species of Cetacean.

So why is this research of importance? For a start it gives biologists new insight into how phenotypic traits can have great similarities, yet still be from completely unrelated species. This research can potentially explain some of the problems evolutionary biologists face. For example when analysing the genome sequences of different species for relatedness, and finding unexpected similarities, which until now would have suggested homology. This research could be taken one step further by measuring tissue-specific gene expression levels, which would not only improve our understanding of how protein-coding genes may converge, but also our overall ability to identify and understand gene regulation at the molecular level.

 

Reference: Parker et al, 2013 Nature

The Origin of the Tasmanian Devil Clonally Transmissible Cancer

by Elena Shanti Franchina

 

The transmissible cancer known as devil facial tumor disease (DFTD) has endangered the devil population in Tasmania, causing its number to collapse since 1996, date when it was first observed in northeastern Tasmania.

An international team of scientists led by Elizabeth Murchison, an investigator at Cold Spring Harbor Laboratory (CSHL), have discovered that the deadly facial tumors decimating Australia’s Tasmanian devil (Sarcophilus harrisii) probably originated in Schwann cells, a type of tissue that insulates and protects nerve fibers. The discovery comes from the effort of the team to carry out a genetic analysis of tumor cells. Based on these data, scientists have identified a genetic marker to accurately diagnose the DFTD.

The DFTD is a unique type of cancer: it is derived from neuroectoderm and is composed of undifferentiated round to spindle-shaped cells with few defining ultrastructural features. The genotype of all DFTD-tumors is similar across all loci, regardless of location, sex or age of the devil. One of the features that make this tumor nothing like previously described devil cancers is the fact that cancer cells are transmitted horizontally from animal to animal through biting. Biting is a normal part of the devil’s behaviour, involved in simple play and reproduction, this is the reason why the disease is highly spread among the population. This mechanism resemble that involved in canine transmissible venereal tumor (CTVT) and a transmissible sarcoma affecting Syrian hamsters, still this type of cancer remain unique in some of its features.

The tumor affects the face and mouth primarily, and lead to death by starvation or due to metastasis to internal organ. So far, no diagnostic tests or vaccines are present for DFTD, and models predict the disappearance of the Tasmanian devils within 25-35 years, due to this disease. “Our discovery is a major step forward in the race to save the Tasmanian devil from extinction,” notes Dr. Murchison, who points out that this research has provided a method to distinguish the DFTD from other cancers that affect the marsupial, allowing easy identification and isolation of affected animals.

The analysis presented in this study, propose that DFTD likely originated in the Schwann cells of a single devil. Schwann cells are found in the peripheral nervous system and produce myelin and other proteins essential for the functions of nerve cells in the tissue.  25 tumors were sampled in the process and they were all found to be genetically identical. Using miRNA deep sequencing and transcriptomes, a match was found for Schwann cells, revealing high activity in many of the genes coding for myelin basic protein production. Moreover several marker were identified, that may enable a more accurate discrimination of DFTD from other types of cancer and may eventually help identify a genetic pathway that can be targeted to treat it.

The researches also compiled a catalog of genes that may influence the pathology and transmission of the tumor, and can help develop a DFTD preclinical test and vaccine. Also further compared analysis of the DFTD and the canine clonally transmissible cancer, could lead to deeper insights in their occurrence, evolution and biology, potentially helping saving the devil from extinction.

 

 

Journal Reference: Science, DOI: 10.1126/science.1180616.

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