Sunday, May 6, 2018

So long and thanks for all the fish : Does the bottlenose dolphin demographic history have a message?

Bottlenose dolphins have enthralled human beings by their amazing performances in dolphinariums and have been part of popular culture becoming the most popular of all dolphin species, while also stimulating public concern over the welfare of display animals. The song "So Long, and Thanks for All the Fish" has established a cult following for this species. 

The genome of the common bottlenose dolphin Tursiops truncatus was sequenced during the boom days of the genomics era when assembling a genome was still considered cool. This initial effort was part of the 29 mammals project. However, we have long since passed that point. So, by the time Yim et al., sequenced the genome of the Minke whale, it was standard practice to look at aquatic adaptation in numerous related species. In addition to looking at coding level changes, they cleverly "Estimated whale population size history". Existing cetacean genomes were also roped into this analysis of effective population size history.

Of the four genomes analyzed in the Yim et al., paper the most surprising result was seen for the bottlenose dolphin that showed an increase in Ne that started at the beginning of the ice age. If this pattern were true it could have interesting implications for understanding the effect of climate change on the demographic history of species. In our preprint titled "Population genomic analysis reveals contrasting demographic changes of two closely related dolphin species in the last glacial", we delve into bottlenose demographic history. 

Few key highlights of our manuscript:

  1. In addition to analyzing the genomes of four common bottlenose dolphin individuals from the public sequencing repository (SRA), we also sequenced four genomes of Indian bottlenose dolphin individuals. The comparison of these 8 genomes shows contrasting demographic changes in the two sister species. 
  2. We use 3 different programs (PSMC, MSMC & SMC++) to reconstruct the demographic history of both dolphin species.
  3. After reconstructing the changes in effective population size, we use the pseudo-diploid analysis of all pairs of these 8 genomes to analyze 28 pseudo-diploid genomes. Based on this we estimate the split times between species as well as between populations within species.
  4. For all our analysis we perform quality control to ensure robustness of our results. Repeat regions are identified using repeat masker program and masked out. Coverage of each individual genome is considered to rule out the possibility of coverage dependent biases in results. Although mutation rate and generation times are fairly well-known for cetaceans, we looked at the combinations of 4 mutation rate estimates and 4 generation time estimates. We find that the main conclusions remain unaltered even after varying all these parameters.
  5. Considerable effort is spent on optimizing the settings of the PSMC program. First, the bootstrap analysis is done with 100 bootstraps for each individual to look at within genome heterogeneity. Next various setting for the -p parameter was tried out to have sufficient resolution in the PSMC results while also having a sufficient number of recombination events after 20 iterations of the program.
It is worth noting that the field of population size history estimation has matured well. New methods that are able to estimate Ne in more recent times have helped answer many questions that were not possible to answer with older methods. For example, the recent analysis of the Tibetan frog (Nanorana parkeri) genome using both G-PhoCS and PSMC brings traditional demographic analysis together with PSMC which had made its way into genomic papers all by itself.

A truly new direction to use of effective population size histories is presented in a preprint posted on biorxiv titled  "Comparative demography elucidates the longevity of parasitic and symbiotic relationships.". Despite the immense potential in using comparative demography to answer questions in studying parasitic and symbiotic relationships, it will be interesting to see how robust these inferences are and whether they can be supported by independent sources of evidence. Our study on dolphins also explores this aspect of the contribution of predator and prey abundance on population size. After sitting on biorxiv for over a year, it is finally out as a letter in MBE.

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