1. Sun et al. 2017. Frontiers in zoology
Comparative genomics analyses of alpha-keratins reveal insights into evolutionary adaptation of marine mammals
Sun et al Frontiers in zoology

2. Marine mammals
Ancestors of terrestrial relatives returned to the ocean on separate occasions and adapted to living all or part of their lives in water.
Despite their independent evolutionary origins, they share morphological (e.g. streamlined shape, paddle-like limbs) and physiological (e.g. Superb diving skills, echolocation, thicker blubber) adaptations for aquatic life.
Cetaceans
Sea otters
Polar bear
Pinnipeds
Sirenians

3. Hair One of the main innovations in mammalian evolution.
Protects from mechanical injuries, facilitates homeothermy, sensorial functions, sexual dimorphism, etc.
No Hair (completely aquatic)
Dense under fur + guard hairs (most time on land)
Dense fur (most time on water)
Little hair + thick blubber (most time on land)
Thin fur coat except around flippers

4. Hair
Strongly keratinized tissue mainly composed of alpha-keratins and keratin associated proteins (KARTAPs) unique to mammals. Type I and Type II keratins.
Encoded by large number of multigene families arranged in cluster on chromosomes.
Previous studies have shown that expansion, contraction, and pseudogenization of KARTAP gene families are related to hair diversity.
Genetic bases of hair evolution in these clades of marine
mammals remains poorly examined.

5. Methods Outline
Scanned α-keratins repertoire from 11 genomes of marine mammals.
Compared them to their terrestrial relatives.
Tested for differences in α-keratins gene retention between baleen and toothed wales (cetaceans).
Tested for gene loss and pseudogenization in full aquatic cetaceans and sirenians (convergent hair- loss phenotype).

6. Methods
Identified α-keratins genes in cow using all known α-keratins genes of humans as queries (BLASTN & TBLASTN).
Accuracy of the sequences verified using GENEWISE prediction.
Putative α-keratins from cow were used to explore and annotate the α- keratin multigene families in the 11 genomes:
Bowhead whale (150x coverage)
Minke whale (92x)
Sperm whale (75x)
Yangtze river dolphin (115x)
Killer whale (200x)
Bottle nose dolphin (30x)
7. Yanftze finless porpoise (NA )
8. Weddell seal (82x)
9. Florida manatee (150x)
10. Polar bear (101x)
11. Pacific walrus (200x)

7. Methods
Othologous α-keratins scanned from terrestrial relatives (sheep, cow, panda, alpaca, elephant).
Newly annotated gene sequences were used as queries in searches against own genome.
Identified α-keratins were classified as intact, incomplete, and pseudogenized genes (according to amino acid alignment).
All KARTAP genes in mammals have a single exon. Homologous fragment of KARTAP genes was used to scan to all genomes. Newly annotated gene sequences were used as queries in searches against own genome.

8. Methods
Phylogenetic tree of genes reconstructed to classify them as Type I or Type II α-keratins.
Mapped α-keratin gene organization to each genome.
RDP4, RDP, Geneconv, Bootscan, MaxChi and Chimaera software to detect gene conversion and recombination.
CAFÉ v3.0 to perform analysis on the evolution of gene families: changes in size, gene gain and loss rates, average contraction and expansion. All from a phylogenetic approach (gene trees).

9. Major Results and Conclusions
Genome regions containing α-keratins are very conservative with special flanking regions of two clusters.
Type I: SMARCE1 & E1F1

10. Major Results and Conclusions
Genome regions containing α-keratins are very conservative with special flanking regions of two clusters.
Type II: FAIM2 & EIF4B

11. Major Results and Conclusions
Marine
Av. of α-keratins
Av. pseudogenization rate = 18%
Cetacean pseudogenization rate = 29%
Manatee pseudogenization rate = 8.3% 56 α-keratins in pinnipeds and 58 α-keratins in polar bear.
Terrestrial
Av. of 58.8 α-keratins
Av. pseudogenization rate = 7%
Artiodactyla pseudogenization rate = 8%
Elephant pseudogenization rate = 10.7% 60 α-keratins in panda.
Similar evolution patterns in polar bears, pinnipeds and their terrestrial relative is likely due to having abundant hair to keep them warm while on land.

12. Major Results and Conclusions
Toothed whales
Av. α-keratin genes = 35
Pseudogenization of follicle-specific keratin genes = 42.8%
Baleen whales
Av. α-keratin genes = 43
Pseudogenization of follicle-specific keratin genes = 35.3%
Higher number of intact functional keratin genes in baleen whales maybe associated with the presence of the keratinized baleens.

13. Major Results and Conclusions
Cetaceans
Completely aquatic with hairless phenotype.
Notable reduction of keratin genes and higher rate of pseudogenization vs. artiodactyls.
Sirenians
Comparable numbers of keratin genes and pseudogenization rates vs. elephants.
Both groups share the loss of gene subfamilies K39, K9, K29, K42 and k74 which are all related to hair development.

14. Questions
If the loss of specific gene subfamilies (K39, K9, K29, K42 and k74) can account for the hairless phenotype in both cetaceans and sirenians, why do cetaceans have lost function in other gene subfamilies as well? For what evolutionary purpose?