Can genomics save endangered species?

 

Nowadays genomics is pervading many research fields in biology, and conservation biology is not an exception anymore. The Giant panda was perhaps the first organism selected for sequencing in which the primary reason was its status as an endangered species. Since then, other species have been selected for sequencing, in an effort to contribute to their conservation. To name a few: the Californian condor, the Tiger, Tasmanian devil and the Iberian lynx, are also entering the genomic era. Our group is contributing to the efforts of sequencing and analyzing the Iberian Lynx genome, an emblematic predator of our peninsula which has the dubious honor to be the most endangered feline species on the planet. With a population below 400, a fragmented and restricted distribution area and a dangerously low level of genetic diversity, its situation is rather critical. Two years ago a consortium of Spanish research groups joined forces to sequence this species' genome. 

"Candiles" the sequenced Iberian Lynx male 

 

I have been asked many times if this effort will definitely save the species, or even whether the money would not be better invested in other efforts. How can a genome help in saving an endangered species?, are we feeding unreasonable expectations on the possible role of genomics in species conservation? Although only time will tell whether such efforts will pay off, I consider that genomics can certainly provide a new, very useful angle to species conservation. In any case, genomics should be considered just as another tool towards species conservation, rather than as the definitive solution. Species are endangered because of various causes, mostly territory loss and degradation, overexploitation, and alteration of their ecological networks. It is obvious that the main focus should be given to fight the causes that triggered population drops and create the necessary conditions for the populations to recover safely. As a powerful tool to understand a species' biology, and as a way to investigate past and current population dynamics, the availability of a genome can greatly help in understanding some of the factors that may have been decisive in population decline. Having a reference genome opens the door for a closer genetic monitoring of wild populations, not only because it enables the selection of new marker genes than can be sampled in many individuals but also because it paves the way for obtaining whole genome-level population data by re-sequencing strategies. Indeed, our project includes already re-sequencing of additional individuals from the main fragmented territories occupied by the species.

Having such kind of data is key to understand gene flow among the different populations, since it will provide a better picture of the genetic pools of the different populations. This will help to better plan crosses among captive individuals -mainly those with permanent injuries that cannot be successfully released to the wild- and future releases of their progeny. This will have a direct impact in the case of the Iberian lynx, where high levels of inbreeding and low genetic diversity exposes fragmented populations to a higher rate of diseases with a genetic basis (particularly a renal disease), and a reduced potential to overcome potential infectious diseases. A better knowledge of the genetic pool of both wild and captive populations will undoubtedly help in guiding strategies to help them recover. In addition individuals and their territories could be tracked from materials such as faeces or hairs.  Other applications may be more specific for a particular endangered species, for instance in the tasmanian devil, genomics has been used to track a transmissible cancer that causes a facial tumor disease that is transmitted by biting. 

Tasmanian devil with transmissible facial tumor

Other applications of conservation genomics that go beyond the sequencing of the endangered species itself, refer to the monitoring, using similar genomics tools, of important pathogens or symbionts of endangered species. Of course all these efforts will only be of little help if the causes that drove their decline are still around. Thus there is a growing number of promising possible applications of genomics to the conservation of endangered species, some of them already at work. I expect this field to grow fast in the coming years, as a concerned scientist I am proud that my particular corner of expertise can contribute to the noble cause of helping to keep the biodiversity of our planet.

Diversity arises whenever, wherever, and at whatever rate is advantageous

 This is the conclusion from a recent paper from the group of Mark Pagel, in which they analyzed a dataset of body sizes of 3,185 extant mammals in a phylogenetic context.

  They modeled the evolution of body sizes across the  phylogeny using a Bayesian approach that allows evolutionary rates to vary at every branch. 

This provided them with an idea of where burst of evolution (big shifts in sizes) had occurred. The main idea was to contrast a long-held hypothesis that the early radiation of mammals was accompanied by increased rates of body-size variation (i.e burst in species diversity coincided with burst in body-size). This was explained by the idea that mammals expanded into a largely-unoccupied niche which provided opportunities for diversification. When the niche was filled up, diversification and evolutionary rates decreased. 

  Results from this team are in stark contrast with such view, since they see bursts at many different places of the phylogeny, which are uncoupled with the early radiation of mammals. 

 Reading this paper was very useful to me since, I was by then preparing the evaluation of a PhD thesis by Victor soria-Carrasco (see some related paper here) on, precisely mammalian, diversification. In the thesis they found that most mammalian orders showed a decline in the rate of diversification (in terms of forming of new species), which may seem compatible with the idea of a niche being filled-up. This highlights the importance of properly delimiting what evolutionary rates we refer to (sequence variation, variation in some morphological character, speciation rate...), since we may reach apparently different conclusions. Complicating the issue further, one does not know whether niche limitation may select for or against diversification. 

 In any case it is comforting to see that the increasing amount of genetic, phylogenetic, and other type of data, as well as sophisticated models, enable us to explore such interesting issues at the edge between evolution, phylogenetics and ecology. I was really impressed by the works mentioned. 

Marine genomes

Craig Venter's team hits again with another large-scale sequence survey. This time they report on 197 complete prokaryotic genomes from the surface ocean's plankton. Note this means roughly a 15% increase in the total number of fully-sequenced species that was available this far. What is perhaps most notable, however, is that these species belong to a largely unexplored part of earth's microbial diversity: that living in the open ocean.

They divided the sequenced genomes into two sets: 34 that seem to be ubiquitous and abundant (present in most ocean samples), and 163 that appeared only at few locations, and compared their genome contents. Widespread planktonic species seem to have reduced genomes, with several functional classes such as gene regulation, cell motility, and membrane transport highly reduced or nearly absent. 

"cryptic escape"
In light of such differences, they propose that these ubiquitous species with reduced metabolic flexibility has adapted to survive in the open ocean by "becoming invisible", that is, reducing their size and metabolism to scape from predators and survive in a poor environment.

Altenative forces driving genome reduction
It is unclear whether reduced cell density can actually serve to scape predation from viruses or plankton-grazing organisms, and this hypothesis needs further testing. This first survey only looks at big numbers, and it is for certain that future more in-depth analyses may reveal more clues on what adaptative strategies are represented by these genomes. One interesting aspect is that forces driving genome reduction here should be different from those experienced by pathogens and endosymbionts, which constitute the best studied cases of genome reduction. In contrast to pathogens and endosymbionts, which live in rich and protected environments, marine prokaryotes thrive in one of the poorest environments with respect to nutrients. Therefore it would be very enlightening to look for differences and parallelisms in these two different adaptations that resulted in streamlined genomes.