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Hawaiian monk seal

Unlike most pinnipeds, monk seals are found in temperate subtropical oceans. There are currently two species in two genera, Neomonachus schauinslandi in the Hawaiian archipelago and Monachus monachus in the Mediterranean. Until it became extinct by the 1950s, a third species Neomonachus tropicalis was found in the Caribbean and evidence suggests that they and their Hawaiian cousins diverged with the closing of the Isthmus of Panama.

Today, monk seals are endangered and the Hawaiian seal has been the subject of a NOAA led recovery effort. As a consequence of that program and the efforts of volunteer and non-profit conservation groups (see and the species is slowly recovering. Together, these groups monitor animals, tag pups and provide veterinary care to animals that are injured or in need of medical intervention.

“Benny” the Hawaiian monk seal enjoying a long, undisturbed nap on a beach on Oahu. Photo by Alan Scott.

We sequenced a particular Hawaiian monk seal named “Benny” who lives largely in the waters around Oahu. I was introduced to Benny on a nature tour of the island in 2009 and was amused that he had been cordoned off with stakes and tape that looked a bit like a crime scene. Benny was sound asleep and oblivious to tourists taking pictures of him. I happened to be back in the same area the next day and stopped out of curiosity to see if he was still there. Not only was he there but in exactly the same location and looked like he had not moved a muscle. This led me to follow his exploits and over the years I learned that he was the subject of a coloring book about keeping the beaches clean and had been captured at least twice for emergency medical procedures after swallowing fish hooks. The latter was an opportunity to get blood samples shipped to Baltimore where we isolated DNA and over the past several years have used it to test various methods of genome assembly including linked-read sequencing (

Recently, we joined the linked-read sequencing assembly with some Hi-C data to generate the chromosome-length genome assembly, now available on DNA Zoo website and soon to appear on NCBI.

We expect that Benny’s sequence will help with conservation efforts (e.g., he has a very low level of heterogeneity across his genome and in his MHC loci that may make him susceptible to disease) as well as let us better understand the evolutionary relationships between seals and other carnivores.

The Hawaiian monk seal genome assembly is the 4th Phocidae (earless seal) genome assembly on the DNA Zoo website, after the Northern elephant seal, the bearded seal and the harbor seal. Check out below the whole-genome alignments between the 4 species. The earless seals appear to have a highly conserved karyotype, with 1 fusion apparent in the harbor seal as compared to the other 3 seal species.

Whole-genome alignment plots between the new genome assembly for the Hawaiian monk seal (Neomonachus_schauinslandi_HiC) and those for the bearded seal, the harbor seal and the Northern elephant seal (Erignathus_barbatus_HiC, GSC_HSeal_1.0_HiC and Mirounga_angustirostris_HiC).

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